Allegiances
by LMXB
Summary: Set after the end of season 3, as Kara and Alex try to overcome everything that happens to them, they find themselves in the middle of new dangers. Dangers which causes everyone to question their allegiances.
1. Chapter 1

**Disclaimer** : I don't own Supergirl or the characters. This is written purely for fun.

 **A/N:** This is set after the end of Season 3. I have made some assumptions about what happens, so at the start of this story the following is true:

 _1\. Lena knows who Kara is (and Kara knows she knows), but they have had a huge fight and Lena looks like she has turned/is turning to the dark side._

 _2\. Mon-El has gone far far away. You can chose if that is to the future or somewhere else - he won't be part of this story._

 _3\. Sam is not dead, but is not part of this story._

 _4\. Ruby is not living with Alex._

 **Synopsis** : Set after the end of season 3, as Kara and Alex try to overcome everything that happens to them, they find themselves in the middle of new dangers. Dangers which causes everyone to question their allegiances.

* * *

"You okay?" Alex asked as she sat next to Kara on the couch.

"No." Kara said pulling her knees up to her chest.

"Come here." Alex said pulling Kara into a hug.

"Sorry." Kara apologised.

"For what?"

"The last few weeks have not exactly been easy on you either."

"Worse on you." Alex said.

"I'm not so sure." Kara said. "I think it was worse for you. I just wish I could be as strong as you."

"You are strong. You're Supergirl." Alex said. "Without trying to sound like you, don't give up on Lena, especially if you buy the Back to the Future theory of time travel."

"You got me a DeLorean so I can go back and fix everything?" Kara asked pulling away from Alex.

"No." Alex smiled. "I meant in that film when Marty changed history it was immediately obvious in the past as the photo changed."

"Not following." Kara said.

"Mon-El was only able to be on Earth because L-Corp created a cure in the future. If Lena really has turned why would any future version of L-Corp help aliens and if L-Corp didn't create a cure Mon-El would have started getting ill...actually he would have died."

"The cure is four hundred years away, anything can happen. Someone else could buy up L-Corp." Kara argued.

"Or L-Corp continues on the same path as Lena tried to set it up on." Alex said.

"Even if that is true, she lied about having Kryptonite. She lied about having the ability to make it."

"And we lied to her about working for an organisation that was trying to hunt her mother. An organisation that kept Kryptonite and used it on you." Alex argued.

"Do you trust Lena?" Kara asked.

"No." Alex confessed. "But I never really did. But Lena was your friend, you trusted her when no one else did."

"Why do all my friends lie to me?" Kara asked. "Lena about Kryptonite, James about Guardian, Winn about Siobhan."

"It's a human thing." Alex said. "But if I believed any of them had lied to hurt you I would have taken them out."

"Thank you." Kara said smiling slightly. "Do you think J'onn can handle things for a few days?"

"Sure. Why?"

"I need some time away from here. I was thinking of going to my cousin's fortress."

"Want me to come?"

"I need some time alone." Kara said. "I'll be back for work on Monday, I promise."

"You sure?" Alex asked.

"I am."

"Do what you need to do, I handle J'onn." Alex said.

-00-

"A break could do her good." J'onn said the following day as Alex explained about Kara.

"I hope so." Alex said.

"A break could do you good as well." J'onn pointed out.

"We could all use a break." Alex said. "But Kara said she wanted time alone."

"I meant you could take a few days for yourself." J'onn offered.

"I'd get bored." Alex shrugged. "Besides someone has to train the new recruits."

"Don't push them too hard. At least in their first week." J'onn said as Winn burst into the room.

"Hey guys. I don't know if it is anything but there was a report this morning of some weirdness at the old psych hospital on the East side."

"Define weirdness." J'onn said.

"Sounded like something out of poltergeist."

"Probably kids messing around." Alex said.

"But it could be something else." Winn pressed.

"When did you start believing in ghosts?" Alex asked suspiciously.

"I don't." Winn said. "Okay fine...always. But this is the first time I have had access to the tools I need to investigate."

"Stay here. I'll take him." J'onn said to Alex.

"Really?" Winn asked happily as Alex mirrored his word, but the tome full of doubt.

"Really. Besides you need to train the new recruits." J'onn said.

-00-

"Again." Alex ordered waiting for the recruit to pick themselves off the floor. "This time don't make it so obvious."

"Just need a minute." The recruit said still on their knees.

"You going to say that to the aliens trying to invade this planet?" Alex asked.

"No." He said as Alex heard some muttering from the other recruits.

"Problem Clarke?" She asked staring at one of the other recruits.

"No ma'am." He replied.

"Sounded like a problem. It sounded like you were saying Supergirl would buy you the time you needed to recover."

"You heard that?" He asked sensing trouble.

"Always pay attention to your surroundings." Alex said looking round the group before saying. "Yes Supergirl can buy us time, but she is not our shield. Officially she doesn't work for this organisation. Out there, in battle, you depend on yourself and you depend on your team. Sometimes Supergirl won't be part of that team so get used to fighting like you mean it." She went on as the door opened.

"Sorry to interrupt ma'am." Vasquez said. "But you are needed in the med bay now."

"Keep sparring." Alex ordered as she followed Vasquez out of the room. "What's wrong?" She asked.

"It's the Director." Vasquez said. "He was hit by some sort of weapon."

"How bad is he?"

"I don't know. He is being brought in now. All I know is he's unconscious." Vasquez explained.

"And Winn?"

"He's fine as far as I could tell."

"Get a team ready, I want that hospital secured." Alex ordered.

"Yes ma'am." Vasquez said returning to the control room moments before J'onn was wheeled through the DEO on a gurney. When he arrived in the infirmary Alex immediately started running tests. As she did so she looked at one of the Agents who had brought J'onn in and asked.

"What do you know?"

"Not much. There was some sort of energy weapon that fired at the Director moments before it exploded. As soon as he was hit he went down and has been out of it since then. Winn is still at the hospital trying to collect evidence."

"I can't see any wound." Alex said "Where was he hit?"

"On the torso. But the energy didn't seem to hurt him. I mean it did as he went down, but there was no wound and no damage to his uniform."

Frowning Alex started a more thorough examination.

-00-

"How is he?" Winn asked as he entered the infirmary three hours later.

"He seems to be in a coma. Physically there appears nothing wrong with him, but he won't wake." Alex said. "Did you manage to salvage the weapon?"

"I have every piece that was left….whether it is enough to figure it out I don't know, but I'm getting right on it."

"Before you do, what exactly happened?"

"We went to the room where all the activity had been reported. Billings entered first and everything seemed fine. I went in and started running scans. There was nothing out of the normal. Then all of a sudden there is a spike in my readings and J'onn is blasted."

"When did J'onn enter the room?" Alex said.

"I don't know exactly." Winn confessed.

"Could it have been his presence that triggered the weapon?"

"Maybe. I can go through the logs in more detail." Winn said. "And it would explain this." He added handing Alex his tablet which displayed a Martian symbol. "It was in the room."

"Looks like they wanted J'onn to go there." Alex said. "Concentrate on the weapon, I'll do what I can here." She continued before adding. "This isn't your fault."

"He only went there because of me." Winn said.

"As soon as he had heard about the symbol he would have gone anyway." Alex said. "Right now we have to figure out what happened and how to fix it. We can worry about stopping something like this happening again later."

"Okay." He nodded before asking. "Do you want me to try and figure out a way to contact Kara?"

"No. She needs a break and currently there isn't much she can do." Alex replied.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing


	2. Chapter 2

**A/N:** Thank you for the comments.

 _Guest(1)_ : I've tried not to make too many assumptions about what may happen to allow readers to pick their preferred path to the end results I listed. Based on what you have assumed the only one that really won't fit with this story is Lena has not been badly injured. Some of your other assumptions don't quite fit with the direction this story is going, but hopefully things will become clear soon.

 _Whalegang34_ \- Thanks! I'll try to update (almost) daily.

Guest (2)- this one will be significantly shorter than some of my recent efforts. ..but I hope you will enjoy it

* * *

"Any change?" Winn asked entering the infirmary three days later.

"No. It's just like after Rhea attacked him. His vitals are erratic and his neurons are working overtime."

"He pulled through back then." Winn pointed out, mainly out of hope as he was still plagued by his own guilt.

"Because of M'gann." Alex said.

"You could take his car to Mars and ask for help." Winn suggested. "For the record that sounded better in my head."

"She may not be able to help. Although it looks the same it could be completely different. Last time she knew he was in trouble and helped. Maybe she hasn't helped this time because she can't." Alex said. "When Kara gets back if he is still showing no signs of improvement I'll ask her to go. In the mean time have you figured out what did this?"

"No. Whoever was behind this made sure the weapon was destroyed in such away we can't reverse engineer it. We were only able to retrieve sixty percent of it. The rest, including the crystal used to modulate the beam, were completely disintegrated. But because I was running various scans at the times I may, I stress may, be able to work out what energy signature it had. Maybe from that you can figure out what effect it would have on him."

"Maybe." Alex said looking distracted.

"Something else bothering you?"

"What's the end game? Did they just want to take J'onn out? I mean it has been three days and there have been no follow on attacks, no other reports of activity using that type of weapon or ghosts. It is like the whole thing was staged to attack J'onn. But why?"

"That I can't help you with." Winn said. "But we'll figure it out." He added trying to sound optimistic before asking. "When does Kara get back?"

"She said you would be back for work tomorrow." Alex said.

"You know she is going to be mad you didn't tell her?" Winn asked.

"I know, but she needed a break." Alex said.

-00-

When Kara flew into her apartment just past midnight she immediately headed for the fridge and grabbed a bottle of water. Walking over to the couch she grabbed her phone and cursed herself for returning so late. Not wanting to disturb Alex, but not wanting her sister to worry she sent a text saying she was okay and suggested meeting for breakfast the next morning. She then put the phone down and headed to the bathroom as a painful sound invaded her head.

" _Hello Supergirl. I hope you had a nice vacation and are well rested...you'll need to be. Before you say anything, this is a one way link, so any not to witty comebacks by you won't be heard. You are probably wondering why I am risking my location to talk to you. The answer is simple, it's time we put our differences behind us and worked together to help humanity. I imagine you don't believe a word I say, which is why I will offer you something as a sign of good faith. Come immediately to the coordinates 39.667 North, 120.998 West, where I will leave a giant sign to let you know you are in the right place. Come alone, without telling anyone and I will let your sister live. If you are not here in the next ten minutes, if you attempt to contact anyone, if you bring your phone or leave a message, I will kill her._ "

Not even waiting for Lilian to finish speaking Supergirl flew through the window of her apartment and flew as fast as she could to the coordinates Lilian had given her.

As she flew over the mountainous forest she saw a green laser shine from the ground into the sky. Assuming that was the sign she followed the laser and landed next to it.

Not seeing anyone she shouted.

"I'm here. What do you -" She started to ask, but before she could finish she was hit by several Kryptonite darts and collapsed unconscious.

-00-

"Winn, I need you to find Kara." Alex said as she hurried over to his station the following morning.

"Did she not come home?" Winn asked as he started typing.

"She did, I think. I mean she sent me a text just after midnight saying she was back and suggesting we meet for breakfast. Only she didn't respond to any of the messages I sent in reply and didn't turn up to breakfast and she's not at her apartment." Alex said as she paced.

"There's nothing on the Supergirl monitor." Winn said. "But her cell phone is at her apartment. Has been since 12:03 this morning."

"Well she isn't there." Alex said running a hand through her hair.

"We'll find her." Winn said.

"Ma'am, I don't know if this is relevant, but radar picked up Supergirl heading out of the city at speed at 12:08 this morning."

"Heading where?" Alex asked.

"All we have is her bearing. We lost contact just after she left the city."

"Pull other resources that were active last night and get a team ready." Alex said.

"Cancel that order." A familiar and unwelcome voice commanded.

"General Lane? What are you doing here?" Alex asked.

"Taking charge of the DEO." He said.

"What?" Alex asked surprised.

"Who else would take charge during the Director's coma?" Lane asked. "You? You disobeyed an order from the President. Two years ago she gave you very specific and clear instructions to destroy the Daxamite vessel. You disobeyed that order, putting this planet at risk. You may have brushed that insubordination to one side, but the President did not. You proved that day that you are not fit to lead any organisation. Consider yourself lucky to have a job."

"Regardless of who is in charge, we need to find Supergirl." Alex said.

"This is not a lost and found department. Our remit is to protect this planet from alien threats."

"We need Supergirl to do that." Alex said.

"Supergirl does not officially work for the DEO." Lane said. "If she has chosen to take a vacation and not tell anyone, it is not my concern. Right now you should be more concerned about the Director, who you sent out into the field with inadequate protection. I am going to get myself settled. I expect a briefing on the investigation into the attack in ten minutes." With that he walked off.

Sensing Alex was about to blow a fuse Winn stood in front of her and said. "Alex." Once he had her attention he said. "I know you want to go out there and search. So do I. But by staying as part of the DEO we can use the resources we have here. It will speed things up. Lane was partially right, J'onn needs you."

"You're right." Alex said forcing herself to calm down. "Tell me when you find something."

-00-

As Kara started to wake she immediately knew she was close to Kryptonite. Trying to ignore the nausea she became aware of her painful arms and realised her arms were chained above her head. Opening her eyes she tried to lift her head up and was rewarded with a smiling Lillian Luthor.

"I was starting to think you would never wake." Lillian greeted.

"Where's Alex?" Kara asked trying to ignore the nausea.

"Alex? I have no idea." Lillian said glancing at her watch. "At work I assume."

"You let her go?"

"I never had her." Lillian said.

"You said-" Kara started sounding confused.

"I said I wouldn't kill her if you came to me. I never said I had her." Lillian explained. "You would have thought, evolutionary speaking, that increased intelligence would have been better than increased strength." Lillian said as she pace round Kara in the small cell, the walls made of some sort fo Kryptonite containing forcefield. "Of course, if your kind had any intelligence perhaps they wouldn't have destroyed their own planet." She added smiling.

"What do you want?" Kara asked.

"I told you. To help save humanity." Lillian said. "But you'll get an extra benefit of being able to help Alex. You claim to love Alex, that she is your sister. If that is true you should want her to be happy. And once you are gone she will be. She can have the life she deserves, not pegged back by you. You also claim to want to help humanity and you will be. The knowledge that we gain from you will help this planet." She said as she injected green liquid into Kara's veins. "And the final benefit is I will get so much enjoyment from this." Lillian said as Kara screamed in pain.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	3. Chapter 3

**A/N:** Thank you for the comments.

 _Guest(1)_ : I am trying not to make too many assumptions about the end of the season...it feels like it os going in the wrong direction, but I am hoping I am wrong.

 _Whalegang34_ \- Thanks!

Guest (2)- In Rising you can take either of the following (I deliberately left it open in case I ever decided to continue): 1. The start of puberty triggered them. 2. It was not the first showing. Ruby started to notice powers during the incident with Coville but ignored them, but their occurrence is starting to get more frequent. 3. In the house there is something from Krypton that Kara brought with her in the pod, that triggered something in Ruby.

* * *

"That's it?" Lane asked once Alex had finished her briefing.

"We deal with the unknown here. We don't have solutions on the shelf. These things take time." Alex replied.

"It shouldn't take this long. He has been in a coma for days, but you don't know why, you don't know how to wake him, you don't know if he is suffering some sort of mental attack and you have no idea who is behind the attack." Lane said. "Based on what you have told me I don't think you are the right person to find a solution."

"Excuse me?" Alex asked asked feeling her rage build again.

"You've had your chance. You've failed. Director J'onzz's care will be transferred to Dr Lyle."

"Who is Dr Lyle?" Alex asked.

"One of my finest physicians."

"Does he have any experience with Martian physiology?" Alex asked.

"This is the perfect opportunity for him to get some. I'm sure he'll ask your opinion if he thinks it relevant." He said. "In the mean time, before you get any ideas about misusing DEO resources to find your cheerleader, I have a job for you. One of the highest importance. Once complete we'll talk about you working on the Director again."

"What is it?" Alex asked.

"As you'll recall the President started a register of aliens. A register that was never completed. By our estimates there are hundreds of non registered aliens in this city. Complete the register."

-00-

Instead of going to her home Alex went to Kara's apartment in the hope she had returned. As she opened the door she called to her sister only to be met by silence.

"Come on Kara. Where are you?" Alex asked before picking up Kara's phone and scanning through the messages again hoping she had missed something. Finding nothing she started to pace the apartment. "Why would you leave?" She asked no one in particular. "Why wouldn't you tell me?...unless you were told not to. But still you wouldn't go without leaving a clue….unless you thought you were protecting someone...me. But still, you're smarter than that. You'd leave some hint." Alex mused as she restarted her search of the apartment. As she searched she realised she hadn't seen something. Guessing she was clutching at straws, but having nothing else to clutch to she left the apartment and jogged downstairs to the mailbox. Opening it she found it crammed full of letters, but none held a clue about her sister's location. Frustrated she returned upstairs and once again picked up Kara's phone and started to recheck the mail. As she scrolled through the inbox a new message came in, it's sender long since dead. Confused she opened the mail.

-00-

"Wha….what...you….doing?" Kara asked as she awoke to find herself strapped to metallic bed.

"I keep telling you. Saving humanity." Lillian said. "I do hope we are not damaging your memory. We still need you functioning. You have such an important role to play."

"What role?"

"I wouldn't want to ruin the surprise." Lillian said picking up a knife with a green blade.

"No." Kara said as Lillian moved the knife to the abdomen.

"I would say this won't hurt….but I would be lying. I'm sure the pain will work as a good anaesthetic….eventually." Lillian said as she pressed the blade against Kara's stomach and started to cut.

-00-

"Anything?" Alex asked as she met Vasquez and Winn in the break room.

"Maybe." Vasquez said. "The night that Supergirl went missing there was a large green laser seen in Plumas National Forest. That National Forest was along the bearing Supergirl was flying on." Vasquez said. "The light lasted one minute and would have been active at the time Supergirl flew over, assuming she kept course and speed."

"You have coordinates?" Alex asked.

"Yes ma'am." Vasquez said handing her a piece of paper.

"You can't go alone." Winn said.

"I don't have a choice. It is not like Lane will help. Besides, I'm not sure he isn't involved somehow."

"With Kara?" Winn asked.

"And J'onn. The timing seems too good." Alex said. "Or maybe I am just being paranoid."

"Something seems wrong with him." Vasquez agreed. "Plus we are all being watched. He distrusts us more than we distrust him."

"If that's the case how are you even going to get out to the coordinates?" Winn asked. "He's not going to give you time off. And you getting fired isn't going to help J'onn or Kara."

"What choice do I have?" Alex asked.

"We can ask James to go."

"And while actually bother looking this time?" Alex shot back.

"He wants to help." Winn said. "I know how worried you are, but if this lead doesn't go anywhere you will be cut off for no reason."

"Fine. But tell James reconnaissance only." Alex said handing Winn the paper with the coordinates on just as the door opened and an army officer walked in.

"Agent Danvers, the General is looking for you. He wants to know how the register is going."

"Tell him, I'm about to get a many more names for him." Alex said leaving the room. Once the officer had left as well Winn looked at Vasquez and asked.

"You sensed that as well?"

"She has a plan and I don't think it's a good one." Vasquez agreed.

"Why wouldn't she tell me the insane plan?" Winn asked.

-00-

As Kara woke she couldn't help the whimper that escaped her lips as burning pain coursed through her.

"I thought you were meant to be the girl of steel." Lillian said. "But clearly all the sticky buns you eat has made you as soft as the butter they are baked with. I considered using your cousin for this part, but in the end settled on you. Obviously not because you are stronger, but when this ends the decision he'll have to make will destroy him like he destroyed my Lex."

"What have you done to me?" Kara ground out.

"Was that the infamous Kryptonian temper beginning to emerge?" Lillian asked. "I do hope so. From what I heard it is quite vengeful. I'd like nothing better to see you embrace your dark side before your cousin kills you. But I am getting ahead of myself. First I have to test how far I can really push you." She smiled before injecting Kara with more Kryptonite.

"Why?" Kara asked before the pain became too much and she screamed out loud.

"Because I need to learn how to play you like a piano….oh and because I can."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	4. Chapter 4

**A/N:** Thank you for the comments.

 _Whalegang34: things will be intense for the next few chapters._

 _Guest 1:_ for once all confusion caused is deliberate. What Lillian is up to won't become clear for a while. With regards to Rising currently I have no desire to continue/ write a sequel. For me the problem with extending it to have ruby dealing with powers is I have done something similar in another story (Although not ruby the concept of a kid dealing with powers)

* * *

"Anything?" Alex asked quietly as she stood behind Winn in the control room.

"Hey Alex, just heard from James." Winn said.

"And?" She asked hopefully.

"Nothing. He saw evidence that someone had been at those co ordinates, but no one is there now. There were tyre tracks, but they disappeared pretty quickly. I'm sorry."

"Looks like plan B then." Alex said.

"Which is?"

"To find her myself."

"Except you can't. If you aren't here Lane will get rid of you." Winn said. "And J'onn does not have the luxury of not having your help. From what I hear they aren't even trying to find a cure right now."

"Which is why I just need Lane to give me a few days off so I can investigate what happened to Kara and J'onn without him breathing down my neck."

"He doesn't seem to be in a giving mood." Winn said.

"I have it covered." Alex replied.

"Want to share?"

"No. It's better if you don't know."

"What have you done?" Winn asked moments before Lane stormed towards them. As he reached them he demanded.

"Agent Danvers what were you thinking?"

"Sir?" Alex asked.

"You accused the wife of a congressman of using slave labour." He stated.

"I did not." Alex said.

"That's not the story she is giving. What the hell did you do?"

"You specifically told me to complete a comprehensive list of non-registered aliens. That is what I was doing."

"What does that list have to do with a congressman and his wife?" Lane asked.

"There are two types of non-registered aliens. The ones who don't trust us and have chosen not to register and those who are effectively slaves and aren't allowed to register." Alex explained.

"I am fast running out of patience Agent Danvers. If there is a point, make it."

"Our research shows that demographic most likely to have aliens as slaves are white, upper and upper middle class. While I did not constrain my investigation to that demographic I did carefully and conscientiously follow leads that pointed to that demographic. Seeing this is not a political organisation I didn't think that would be a problem, especially as I implied I worked for the FBI not the DEO."

"How many leads have you followed?" Lane asked.

"Just nine, today that is. I have another fourteen lined up for tomorrow." Alex replied cheerfully. "You said as soon as I had wrapped this up I could go back to helping J'onn so don't worry I will keep a fast pace on this."

"I have been studying your personnel file." Lane said after a long, drawn out silence. "It makes for disturbing reading. But it does point to you being on the verge of a psychotic break, clearly the pressure has caused you to take leave of your senses. You are suspended from this organisation. You are to leave immediately."

"For how long? I mean the register is important, I'd like to finish it." Alex said as Winn wondered what was going on.

"You may report for duty at o eight hundred, next Monday. In the mean time you are to have no contact with anyone from this organisation and no contact with aliens or anyone associated with the register. And no contact with anyone connected to politics. Do I make myself clear?"

"Yes Sir." Alex said. "See you on Monday."

Confused Lane watched Alex leave before turning to the staff in the control room and said, looking at Winn. "If anyone here has contact with Agent Danvers their contract will be terminated." He then looked at one of his men and ordered. "Initiate protocol Cobra Zulu 532."

"Yes Sir." The Major replied before leaving.

-00-

Waking up Kara was overwhelmed by the pain originating from her stomach. Forcing her eyes open she found herself looking up at a familiar figure.

"Jer...miah." She gasped causing her adoptive father to pause what he was doing and glance at her.

"Not much longer." Jeremiah said before looking down again moments before Kara felt a burning pain spread through her stomach.

"Please. Stop." She begged as the pain became overwhelming.

"Not much longer." Jeremiah repeated as he once again burnt Kara's skin.

"Please." Kara pleaded as she screamed in pain.

"I'm sorry. I have no choice." Jeremiah said as pain got worse, until eventually Kara passed out.

-00-

As Alex reached her front door she saw James standing outside.

"James." She greeted.

"Alex. Hey. Are you okay?" James asked.

"Perfect." Alex said.

"Really, because I heard you were suspended."

"I was." Alex said.

"You okay with that?" James asked wondering why Alex didn't seem more upset.

"I am."

"Okay. Well Winn said you may want some help."

"I'm good." Alex shrugged.

"I know you and Kara lost faith in me, but I can help."

"You did. You searched and found nothing." Alex said. "And although you've said that before I believe that you are telling the truth this time."

"I knew Lena wasn't hiding Kryptonite." James asked.

"Yeah, because she was making it." Alex snapped. "If you weren't comfortable accepting the mission you could have said no. No one would have thought less of you." Alex said. "It was the choosing to lie about it that made us all lose faith."

"So now you are refusing my help out as a kind of punishment?" James asked.

"I need to work with people I can trust. But if I thought for a second you could help Kara I would be asking, even begging for your help. But right now there is nothing you can do." Alex said not wanting to discuss the situation in the hallway or her apartment.

"I can do more. Whatever you're doing you shouldn't do it alone." James said.

"I'm not doing anything alone." Alex said. "But it has been a long day and I need to sleep."

"Okay." James said hurt and confused. "You know where I am if you want anything." With that he left.

Content that she was alone Alex went into her apartment and went straight to the kitchen. She went to the kitchen drawer and pulled out a knife which she rested on the side. She then took a bottle of whiskey off the shelf and gulped some down before taking off her shirt, which she balled up and put in her mouth. She then poured some whiskey over her shoulder, picked up the knife and dug out her tracker. Grunting into the balled cloth in her mouth as she did so. When the tracker was finally removed she dropped the knife in the sink and poured more whiskey on the wound.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	5. Chapter 5

"Agent Schott, where is Agent Danvers?" Lane demanded.

"I don't know. You told me not to have contact with her." Winn replied.

"This is not the time for games Agent Schott." Lane said sternly.

"No games." Winn said. "I've not heard from her."

"Do you seriously expect me to believe that you have had no contact with Agent Danvers for three days?"

"You ordered no contact, I followed your order."

"Then find her Agent Schott."

"Um, okay." Winn said typing on his keyboard before saying. "She's at her apartment."

"Are you sure?"

"Both her tracker and her phone are saying yes." Winn replied.

"Major Riggs, assemble a team and go to Agent Danvers's apartment and bring her here. If you don't find her, tear her apartment to pieces until you find out where she went and who she's with."

"Has Alex done something?" Winn asked, wondering what was going on.

"For her sake she better hope not." Lane said before leaving.

-00-

As Kara half woke she felt searing pain in her stomach. Looking down she saw Jeremiah once more. This time he was holding some sort of metal object to her torso.

"Why?" Kara croaked.

"Just hold on." Jeremiah said. "This will hurt. But it won't last long."

-00-

"Winn." Vasquez whispered as she slid her chair over to him.

"What's up?" Winn asked.

"I think I've figured out why Lane is after Danvers."

"Why?" Winn asked looking at her.

"He got an email this morning with this picture attached." She said showing him her cell phone.

"That isn't good." Winn said.

"You didn't know?"

"Of course not. I've not spoken to Alex since she left. Who sent the email?"

"I don't know. It was from a recently created webmail account. But I will see if I can figure it out." She said as Lane, flanked by four officers, marched towards them.

"Where is Agent Danvers?" He demanded.

"Her tracker is still at her apartment." Winn said looking at his screen.

"Only she isn't. Her tracker was removed."

"By who?" Winn asked.

"I'll add that to the list of questions we'll ask during her interrogation. Tell me everything you know."

"About Alex?" Winn asked.

"Where is she?" Lane repeated.

"I don't know." He replied.

"Every one step back from their workstations." Lane barked, his tone immediately causing a silence to descend. Pausing he looked round to ensure everyone had followed his order before saying.

"This organisation is plagued with ill discipline, a complete lack of respect for authority and an inability to achieve its purpose. That changes today. From this point forward this will be run as a military organisation, people will follow orders and not use the facilities to help their own personal crusades. Working here does not put you above the law. You should be upholding the values of this country not ignoring them. Anyone who disagrees with anything I have just said can leave now. I should warn you, that anyone who choses to stay will be severely punished for not following orders." He then paused and waited for people to leave. When no one did he said. "Good. First task of the day. I want Agent Danvers located and arrested. Agent Schott, you were hired based on your supposed expertise. I suggest to showcase those skills before I reconsider your employment."

-00-

When Kara woke she wasn't sure if it was the nausea or the pain that was worse. Looking down she realised she was lying on the ground, her hands no longer bound. Assuming she was seen as too weak to be a threat she she prayed she was strong enough to escape. Before she even attempted escape though she tried to take in her surroundings. Looking round all she saw was murky darkness. Before she could get too disheartened she heard footsteps and voices. Immediately stilling she lay silently hoping no one would realise she was awake.

"We can do this together. Come with me." A male voice, she recognised as Jeremiah, said.

"What about Kara?" Alex asked. On hearing her sister's voice Kara almost cried. Before she could say anything though the conversation went on.

"This is more important." Jeremiah said. "We need to do this together. Come with me."

"But Kara-"

"Kara can't help us. Come on Alex. It will be like old times."

"Okay." Alex agreed before the footsteps and voices faded before disappearing.

"No." Kara said, her voice barely louder than a whisper. Not hearing Jeremiah or Alex Kara tried to move, only to cause a searing pain to rip through her. Looking down she saw bloodied bandages covering her stomach and she recalled Jeremiah operating on her. "Why?" She asked as she fell unconscious.

-00-

"Have you found her yet?" Lane demanded as he walked up to Winn.

"Alex knows how to go off grid." Winn said.

"Then figure out what the end game is." Lane ordered.

"Perhaps if we found Supergirl, we'd find Agent Danvers." Vasquez suggested.

"Agent Danvers and Supergirl have always been close." Lane mused before turning to Winn and asking.

"Agent Schott, what anti-Kryptonian weapons do we have here?"

"We don't."

"What about Kryptonite?"

"J'onn, I mean Director J'onzz handed it over to Superman." Winn said.

"Can't we make any?"

"Umm…." Winn started as a solider Winn recognised as a former DEO agent said.

"Sir, we established that Ms Luthor can make it."

"Can she? That shouldn't surprise me." Lane commented. "Well then that buys us time."

"Why do you need Kryptonite?" Winn asked, not sure if he wanted the answer.

"As you have all reminded me Supergirl and Agent Danvers are close. Both are missing. I can't rule out the fact that they are conspiring. If Supergirl is assisting Agent Danvers she is considered a hostile entity and will be treated as such. Unless you have some other way of stopping Kryptonians we need Kryptonite."

"But-" Winn started.

"This is not a democracy Agent Schott." Lane snapped. "Go to L-Corp and place an order."

"Me?"

"You are friends with Mr Olsen, who I understood to be close to Ms Luthor." Lane said. "Go, now."

-00-

The next time Kara woke she once again found herself untied and alone. Recalling what she had heard she assumed she had been left to die, or left to be experimented on. Either way she knew she had to leave and find help.

Sitting up she gasped in pain as her side burned. Looking down she wondered exactly what they had been doing, but she knew she did not have time to dwell. Slowly she crawled to the wall and used it to help her get to her feet before she took one unsteady footstep after another until she reached the entrance of the cave.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	6. Chapter 6

**A/N:** Thank you for the comments.

 _Whalegang34:_ Kara isn't being manipulated quite the way you think she is...but things will be explained in a few chapters time

 _Alliedstasis_ : Things will start to get clearer with time...although Jeremiah's status will remain a grey area.

 _Guest 1:_ It does sound like it would fit in really nicely to the end of Rising, but I have a few real life issues that means I probably won't be writing anything new (and long) for awhile (this story is pretty much sitting finished on my hard drive)

* * *

"Winn. What do you want?" Lena asked as she saw him enter her L-Corp office.

"I would like to place an order." Winn said.

"For what?"

"Kryptonite." Winn said.

"Is this some type of joke?" Lena asked glaring at the DEO agent.

"No, but I wish it was. General Lane has taken over the DEO and believes Supergirl to be a hostile entity. He would like to stock up on Kryptonite."

"And you?"

"Am praying you will say no." Winn said honestly.

"Yet you are here."

"If I didn't come he would have fired me. Whilst I have my job I can help Alex and Kara and J'onn."

"Well you can tell General Lane that I am a business woman and a highly successful one. I have no issue in selling him anything he wants. However, I am still owed a lot of money by the DEO for damages to my premises. Once I have been suitably compensated then we'll talk. Also tell him that next time he wants something, talk to me in person or send someone with the authority to make decisions."

-00-

As Alex and Jeremiah came back into the cave Alex immediately headed to where they had left Kara only to find she had gone.

"No no no." Alex said.

"Alex, calm down. She can't have gone far." Jeremiah said.

"What if they took her?" Alex asked. "I knew we shouldn't have left her."

"Alex, look at those marks on the ground. It looks like Kara dragged herself out." Jeremiah said. "We'll find her. Besides there is no one left at that base to come after her. I made sure of it."

"She must have been so scared." Alex said walking out of the cave relieved to find tracks. Not waiting for her father she started jogging along the tracks she hoped Kara had made.

"Alex, be careful." Jeremiah said jogging along side her.

"You just said she left by herself." Alex pointed out.

"I'm sure she was alone. But we don't know the extent of what Lillian did. Kara may be a danger to herself or you. We need to be careful." Jeremiah said.

"How can she be a danger? She is barely alive." Alex pointed out.

"What if she was exposed to Red Kryptonite or Silver Kryptonite?" Jeremiah said. "Anything could have happened to her. She may be hallucinating. We need to be careful."

"There." Alex said ignoring her father's words as she saw blonde hair in the distance.

"Kara!" She called as she scrambled to her sister's side.

"Alex?" Kara asked turning. "You're here?" She asked. "You're real?"

"I'm right here." Alex said.

"No...you left….part of this." Kara said backing away from Alex, looking for a weapon.

"Kara-" Alex started.

"Stay back." Kara said finding a glorified twig and waving it at Alex.

"Kara I don't know what they did, but I'm here to take you home." Alex said, trying to sound calm.

"You left." Kara said.

"I'm right here." Alex said, having no idea what Kara was talking about. Not giving Kara a chance to argue further she moved quickly and wrapped her arms round her sister.

"It's okay, I'm right here." Alex whispered.

As Kara started to take comfort from Alex's presence she saw Jeremiah standing a few feet away. On seeing him she started to lash out, landing a couple of blows on Alex before freeing herself of Alex's hold.

"Stay back." Kara said.

"Kara, it's okay." Alex said holding a hand to her stomach where Kara had just punched her.

"Kara sweetie, you're hurting yourself." Jeremiah said seeking blood soak through the bandages.

"Stay away." Kara said backing into a tree.

"Kara, it's me Alex. I would never hurt you. We need to get you back."

"No, not going back. Just let me die."

"You are not dying." Alex said firmly pulling Kara into her arms and holding her. When Kara stilled Alex pulled back in panic.

"It's okay, she's passed out." Jeremiah said. "She must be exhausted and in so much pain. Let's get back to the cave." He added as he scooped Kara up. As he walked off with Kara Alex pressed her hand to her side. Feeling the wetness she lifted up her shirt and saw the blood. Quickly checking it wasn't deep she lowered her shirt and hurried after her father.

-00-

"How is she?" Jeremiah asked as he handed Alex some water later that evening.

"I've stopped the bleeding but she's burning up and there is still no signs of her powers. We're not winning this battle. We can't do this alone any longer. We have to get her help."

"But where? Do you really think Lane would help? That's even assuming he didn't hand her straight back." Jeremiah argued.

"I can think of one place that no one would think of looking that probably has better equipment than the DEO."

"Really? That's great."

"Maybe not. Getting in maybe a problem." Alex said. "And once we're in it will probably be a hostile negotiation."

"I'm sure you can do what needs to be done. You've always been good at that."

"I'm not sure how safe it will be for you." Alex said.

"We're in this together." Jeremiah assured her. "I'll uncover the car, get Kara ready."

-00-

"Lena." Alex said as she stepped out of the shadows in the parking lot.

"Alex? Why are you here?" Lena asked. "I can't believe you are here to do Lane's bidding."

"Lane's bidding?"

"Buying Kryptonite." Lena replied.

"He's what?" Alex asked eyes wide.

"You didn't know?"

"No. I'm not exactly employed by the DEO at the moment." Alex replied.

"Hence the hiding in the shadows." Lena guessed. "Then why are you here?"

"I need your help."

"Why would I help you?"

"Kara needs help." Alex said.

"And I would help because?"

"You are her only chance."

"Be that as it may, Kara made it quite clear she wanted nothing to do with me."

"Well you weren't exactly innocent in all that." Alex said. "Please, if you don't help, Kara will die." Her words causing Lena to pause before finally asking.

"What exactly do you want from me?"

"Access to one of your labs. She needs medical help."

"Then go to the DEO."

"I can't. Especially if Lane is stockpiling Kryptonite." Alex said. "Please she needs help now." When Lena did not offer her assistance Alex went on. "If you don't want to do it for Kara, what about doing it to cancel out your debt. You owe Kara your life. And if that isn't enough to help her, name your price and I will do whatever you want."

Sighing Lena scribbled something down on a piece of paper, which she handed to Alex. Seeing Alex's confusion she said. "It is obvious you don't want anyone to know about this, so let's use a lab no one knows about. Get Kara there and I will do what I can."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	7. Chapter 7

**A/N:** Thank you for the comments.

 _Whalegang34:_ It will take Kara a long time to recover from what has happened.

* * *

"Agent Schott. Have you located Agent Danvers yet?" Lane demanded, his mood worse than normal.

"No Sir."

"Why not?"

"She is completely off grid. Not even using her credit cards. She knows how to hide. We just have to wait for her to make a mistake….or if J'onn recovers he may have some insight."

"Don't expect anything from Director J'onzz." Lane said before asking. "What about CCTV?"

"I have set up facial recognition, but so far nothing."

"What about her family?" Lane asked.

"Her family?"

"Has she contacted them? She has a mother and a sister doesn't she? Are you monitoring them?"

"Yes. She has not made contact." Winn said.

"If you haven't located her in twenty four hours bring her family in for questioning."

"On what grounds?"

"National Security." Lane said before marching off.

"What's wrong with Lane?" Winn asked Vasquez.

"His request for extra budget was turned down meaning he can't pay off Lena. Apparently the congressman that Agent Danvers annoyed holds a lot of sway." She explained without looking up from her console. "Any news from Agent Danvers?"

"No and I am really starting to worry."

"You should worry more about your jobs and less on traitors." Major Riggs commented as he approached them. "The way I heard it all DEO agents are being replaced."

-00-

"What happened?" Lena asked as Jeremiah carried the unconscious and pale Kara into the lab.

"Your mother." Alex said bitterly.

"Her powers?"

"Gone. We don't know why." Alex explained.

"Put her here." Lena said pointing to a bed. As Jeremiah put her down Lena took out various pieces of equipment which she carried over to Kara.

"What the hell did they do to her?" Lena asked when she saw up close just how bad Kara looked.

"We don't know." Alex said. "But whatever they did is still affecting her. She's getting worse."

"She was being held in a Kryptonite cell. They had performed several operations before I got to her. But I don't know what their purpose was." Jeremiah said.

-00-

"You should get some rest." Lena said seeing how tired Alex was looking several hours later.

"Not until I know what's wrong with her." Alex said.

"The latest test results should be ready soon." Lena said. "Until then there is nothing you can do."

"Thank you for helping." Alex replied.

"Why did you really bring her here?" Lena asked.

"There are only three places that have the equipment we need. The DEO, Cadmus and here."

"I understand why you didn't consider Cadmus, but why not the DEO?"

"General Lane has taken charge."

"I heard, but he can't be that bad."

"He hates aliens and I can't be sure he isn't working with your mother. Even if he wasn't there was no guarantee he would help."

"But surely he was a better choice than me."

"Why? I may not agree with your methods, but you are not a bad person." Alex said. "If Lane is working with Cadmus we couldn't risk the DEO. Also if he is working with them we had to go somewhere no one would expect us to go. Where's better then L-Corp?"

"It was still a risk." Lena said.

"Just because you are related to the devil doesn't make you the devil." Alex pointed out. "And if Kara was able to make the decision she would have chosen you."

"No she wouldn't."

"Kara felt betrayed. She fought your corner so many times. We all thought the worse of you, but not Kara. No matter how strong the evidence, she was on your side. Then you just confessed to having Kryptonite. Kara is so trusting and when that trust is betrayed she takes it personally."

"You forgave me."

"Well, I have less faith in people than Kara does. I expect to be betrayed. Kara doesn't. When Kara feels betrayed she lashes out, acts without thinking. She once refused to work for the DEO and J'onn." Alex said.

"Why?"

"He told her he had killed her aunt." Alex said.

"But she forgave him?"

"Because I gathered the courage to tell her the truth. That it was me who killed her. I will never forget the look of betrayal on her face. But it is the only time I have known her to forgive betrayal quickly." Alex said as the monitors attached to Kara started bleeping.

"Kara!" Alex exclaimed returning to her sister's side.

"Her lungs are failing." Lena said looking at the readings.

"I need to incubate." Alex said. Nodding Lena went to a cabinet and fetched the relevant supplies which she placed to Alex's side.

"Come on Kara, stay with me." Alex said as she incubated.

-00-

"What happened?" Jeremiah asked when he re-entered the room and saw Kara on a ventilator.

"Her lungs started shutting down." Alex said.

"We'll figure this out." Jeremiah said concerned with how pale Alex was looking.

"What if we don't? I am meant to look after her." Alex said running a shaky hand through her hair.

"And you do." Jeremiah said. "This isn't on you. But to help Kara you need to get some rest. I'll stay with her and see if I can figure out what they did. Go get some sleep."

-00-

"Anything you want to share?" Lena asked Jeremiah later that evening.

"How do you mean?"

"You worked along side my mother for years. You must have some idea what she did to Kara."

"I haven't been part of Cadmus for over a year." Jeremiah pointed out.

"Yet you managed to learn that Kara was being held at a secret base and rescue her with just Alex on your team?"

"Actually it was just me. Alex didn't join us until I got Kara to safety." Jeremiah said.

"Doesn't make you sound any more innocent." Lena said.

"I keep tabs on your mother's activities. It helps keep me free." Jeremiah said. "When I discovered she was being held I went in and got her out. Unfortunately there wasn't a book left lying round explaining what they were up to. I thought it was safer to get Kara out of there and destroy the facility than dig around the databases. Maybe I was wrong."

"Even if I believed you and you are completely free from my mother you must have some idea what she was up to. You were there for years. Even if things have moved on, my mother's methods and tools will be based on work done when you were there." Lena pointed out. "You need to tell us everything. I can see you are holding back."

"I did things I'm not proud of." Jeremiah said. "If Alex finds out she won't ever forgive me. I'll have lost her forever."

"The fact you are ashamed of what you did places you far higher on the morality ladder than my mother." Lena said. "I get that you don't want to lose Alex, but if you don't tell us everything we may not figure this out and if we don't we are going to lose Kara. And if we lose Kara, Alex is lost as well. You have to tell me everything."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	8. Chapter 8

**A/N:** Thank you for the comments.

 _Guest_ \- they will all put forward their own sides as to why they were hurt/angry/betrayed before this ends.

Whalegang34 - Thanks! It is about to get a little more twisty.

Guest2 - I have not managed to watch the episode yet so can't comment.

* * *

"Lena? What a surprise." Lillian smiled.

"Really?" Lena asked. "And there I was thinking it was all part of your master plan."

"What plan is that?" Lillian asked.

"Alienate me from the world."

"That was all you." Lillian said. "And I know you believe I don't say it enough. But I am proud of you. But why are you really here?"

"What did you do to Supergirl?"

"Why do you think I did anything?"

"Because I've seen the evidence."

"She's with you?" Lillian asked surprised.

"She is. Alex came running to me. Along with an old acquaintance of yours." Lena said.

For a moment Lillian looked at her daughter before guessing who she was talking about. "Jeremiah?"

"Indeed."

"So Supergirl comes running to you and everything she did is forgotten and you embrace her with open arms?"

"Oh no. Our friendship was a lie. She used me to get what she needed and I am more than happy to return the favour. You may be cold, but you don't torture for fun. You had a specific purpose in mind and I want to know what."

"You said you wanted nothing to do with me." Lillian said.

"I don't. But the one lesson you drummed into me since I came to live with you was the importance of the two Ps. Progress and Profit. Knowing you, whatever you were doing can lead to gains in both."

"You know me well." Lillian said smiling. "But what about your fluffy persona you were trying to build?"

"You were right. The world will always see me as a Luthor. I may as well be what they expect. Why waste millions on a vanity project when I can make billions working with you. The world has turned against me. Everyone who ever claimed to be a friend has betrayed me. I'm done trying to make amends. From now on I am working for myself."

"There is hope for you after all." Lillian smiled. "So what else have you been told?"

"They think Lane is working with you."

"Alexandra has always been insightful, but paranoid." Lillian said, neither confirming or denying the claim.

"At the moment Supergirl is languishing in my lab. Jeremiah and Alex believe I am helping her. They also believe that she is dying. If she gets worse they let me do whatever I say needs to be done because they are desperate."

"And if your treatment helps me they'll never know?" Lillian said.

"Precisely." Lena smiled. "But I need to know that what I'm doing is not contributing to something bad. I am not Lex."

"Your work will eventually free us from all Kryptonians and all aliens for ever. No human will be harmed."

"The Medusa virus?" Lena asked.

"Oh no. That is a short term fix, not a permanent solution. What I am trying to achieve is so much bigger. It will free us from aliens for ever. Which is funny."

"Why's that?"

"Because it builds on the Medusa virus designed by the Kryptonians, the plague made by Pestilence and phenomenal strength that Kryptonians get from the sun. You could say the Kryptonians are the architects of their own downfall."

"I thought they were immune to the virus." Lena said.

"They are, but it will be the ultimate killer due to how it mutates in their blood. It was amazing to watch the virus evolve."

"But if the Kryptonians are immune what good does it do?" Lena asked.

"The virus is not for them, they'll be long dead by then. Supergirl will have been killed by Superman who will be broken by what he does." Lillian smiled.

-00-

"How is she?" Lena asked returning to the lab.

"The same." Alex said releasing Kara's hand and looking at the Luthor. "Where have you been?"

"I thought you and your father needed to talk." Lena replied.

"Yeah." Alex replied.

"Where is he?"

"Next door sleeping."

"He regrets what he did." Lena said.

"Doesn't change the fact he did it."

"He may not have had a choice. My mother can be very persuasive." Lena replied.

"There's always a choice."

"Well he's here, helping. That has to count for something."

"I really hope so." Alex said. "But right now it's not getting us any closer to figuring out what is wrong with Kara."

"No. But when I was away I started going over the scans more slowly and I need to ask you something." Lena said.

"What?" Alex asked.

"Is this normal for Kara?" Lena asked showing Alex a spectral analysis.

"No….but I have seen something similar before." Alex said shutting her eyes as she tried to think. "Red K. Her blood work analysis had the same signature. But Red-K doesn't have this effect on her. It makes her angry and free. It doesn't strip her of her powers."

"Could the signature be Kryptonite related rather than Red-K specific?" Lena asked.

"I don't know. Maybe. But it doesn't explain her symptoms." Alex said. "We need to get...to...to get." Alex started.

"Alex? Are you okay?" Lena asked.

"I'm fine...Need to concen-" Alex said before collapsing unconscious.

"What happened?" Jeremiah asked running into the room and seeing Alex sprawled on the floor.

"She collapsed." Lena said as she examined the unconscious DEO agent. "When did she get this?" Lena asked seeing the gash on Alex's side.

"I don't know. It must have been when we found Kara. There was a struggle. I didn't know she was hurt. Why didn't she say anything?"

"Probably because she was more concerned about Kara." Lena said as she examined the wound. "It is definitely infected. She needs real medical help."

"You have access to antibiotics?" Jeremiah asked.

"Of course. We make them five floors up."

"Then give them to her." Jeremiah said.

"I am not a medical doctor." Lena said. "I can give Alex antibiotics, but if it is anything other than an infection they won't help and by delaying real medical care you could be putting her life at risk."

"If we take her to a hospital she'll get arrested."

"But she'd be alive." Lena argued.

"What about Kara?"

"I will do all I can." Lena said. "But you know once you leave with Alex, you can't come back here. It's too risky."

"I know." Jeremiah said reluctantly as he looked at Alex whose breathing was becoming erratic. Turning to Kara he approached his adoptive daughter and kissed her forehead. He then turned back to Lena and said.

"Tell her that I am so proud of her." As Lena nodded Jeremiah scooped Alex up in his arms and walked out. As the door shut behind him Lena walked over to Kara and said.

"Looks like it is just the two of us." Lena said. "Let's get you moved somewhere we won't be found then we can get to work."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	9. Chapter 9

**A/N:** Thank you for the comments.

 _Guest_ \- That was deliberately vague, Lillian's true plan will come out slowly.

Whalegang34 - Not everything is as it seems. But Alex will end up on the warpath.

* * *

"James?" Alex asked confused when she saw Kara's friend standing against a door.

"Hey." He smiled, but didn't move towards her.

"Where am I? Kara?" She asked trying to look round.

"Take it easy." He said. "You really don't want move."

"Why?" Alex asked continuing to scan the unfamiliar room.

"Lane wants to have you arrested for helping Jeremiah." James explained. "He has people outside ready to take you in. The doctors here are standing firm but once they know you are awake and can move they may not be able to stop Lane transferring you to a military hospital. Which is why I'm blocking the window."

"Kara?" Alex asked noticing she was cuffed to the bed frame.

"We still haven't found her. I'm sorry. But you know Winn won't let this go."

"Still not found her?" Alex asked confused wondering how much of her recent memory had been a dream. "How did I get here? Where is here? How long have I been here?"

"A man brought you in. He didn't give a name and wore a hood, but we think it was your dad. You had a really badly infected wound. You've been unconscious since you were brought in two days ago. Eliza is trying to get down, but with the weather she is having trouble." James said.

"Two days?" Alex asked trying to sit up, as she did so she knocked off the heart monitor and triggered an alarm. Moments later several nurses ran in, followed by two military policemen.

-00-

As Alex was deposited in a DEO cell she looked round at the neighbouring cells and saw several aliens she had personally captured.

"I had thought about holding you at my base." Lane said. "But the DEO have more flexible rules on holding prisoners….something you have exploited many times. I also thought you'd appreciate the company you get here. Knowing you are surrounded by aliens who want to kill you should also persuade your friends here not to do anything reckless. Of course you could cooperate and we could move you somewhere more comfortable."

"Cooperate with what?" Alex asked.

"Tell me where Jeremiah Danvers is."

"I don't know." Alex said.

"Have it your way."

"Wait. How's J'onn?" Alex asked.

"That's classified." Lane said before leaving.

Feeling nauseous and cold Alex sat on the bunk and wrapped the blanket round her and wondered how Kara was doing and why Lena and her father had not brought anyone else into help.

-00-

As time went on Alex started to feel more tired and more nauseous. Just as she was considering asking for help she was disturbed from her thoughts by a newcomer stopping outside the cell and greeting.

"You just can't help but find trouble, can you Agent Danvers?"

"Lucy?" Alex asked looking up surprised.

"Hello Alex." Lucy smiled.

"What are you doing here?" Alex asked as the younger Lane entered her cell.

"I am your lawyer."

"I'm not army."

"I know. But Cat Grant pulled a few strings and the President ordered me to represent you."

"Does your father know."

"He does. He took it as well as he did when sixteen year old Lois 'borrowed' his car."

"I hope you're as good as you were." Alex said.

"I'm better, which is just as well for you. The case is not looking good." Lucy replied. "But then again neither are you. Do you want a doctor?"

"No….unless I'd be put in the infirmary next to J'onn." Alex said.

"He's in quarantine." Lucy said. "From the sound of it his condition has not changed. Seriously Alex you look awful, get some rest we can discuss everything else tomorrow."

"I'm not tired." Alex said. "I'd like to know what I'm being charged with."

"In a nutshell, aiding and abetting a known fugitive."

"My father?" Alex guessed.

"Got it in one. And the evidence is damning and shows pre-mediation." Lucy explained.

"What evidence?" Alex asked.

"You left the DEO-"

"Your father suspended me." Alex countered.

"You removed your tracker."

"I was suspended." Alex repeated.

"You went completely off grid for over a week before you end up in hospital with an infected stab wound."

"Not exactly enough to make me America's most wanted."

"True, but the photographic evidence of you with your father, pushes your status to criminal." Lucy said. "Suspended or not, you are a government agent who has a responsibility to enforce justice. Your father is a wanted man and you did not bring him in."

"Aren't you meant to be on my side?" Alex asked.

"I am. That's why you need to know what you are up against. But I have a defence."

"Wow, you are good. You haven't even heard my side. So what is your plan?"

"We could argue you tried to bring him in and he fought back. That's how you got hurt."

"I'm not accusing dad of assaulting me." Alex said.

"I figured you'd say that." Lucy sighed. "So what did happen? Where have you been?"

"Trying to find Supergirl."

"And did you?" Lucy asked.

Believing the room was probably bugged Alex replied. "No."

"Any leads?" Lucy asked.

"No."

"Alex you could be in here a while. In case you haven't noticed my father is not a fan of yours and he is happy to exploit the DEO's loose rules to his advantage. Let me help."

"I didn't find her. I don't have leads." Alex said.

"What about suspicions?"

For a moment Alex remained silent before figuring giving Lucy the name of a suspect might help her figure out the truth.

"Lena Luthor."

-00-

"That wasn't exactly productive." Lane said when Lucy entered his office. "You need to gain her trust so she hands over Jeremiah Danvers."

"How do you know what we discussed?" Lucy asked causing her father to point to a speaker.

"We have microphones in her cell." He explained.

"Alex is my client and our conversations are confidential." Lucy said.

"Her father is a terrorist. She waived her rights when she helped him."

"You don't know she did help him. All you know is there is a photo, which could have been fabricated, that shows her meeting him."

"Don't give me that b.s. she is guilty and you know it. You need to help me put a stop to this."

"No. I need to ensure that Agent Danvers is treated fairly." Lucy said.

"If you prefer I can order you to hand over all-" He started on fully Lucy to interrupt.

"I am outside of your chain of command. You can't order me to do anything. If you have an issue with that talk to the President." With that she walked off.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	10. Chapter 10

**A/N:** Thank you for the comments.

 _Guest_ \- I miss Maxwell Lord and Lucy Lane. Max won't be in this story, but Lucy will have a large role. I really hope at some stage they'll finish the plot they teased at the end of S1.

 _Guest(2)_ \- The full extent of what Lillian did won't become clear until the almost end of the story. It will be awhile before J'onn wakes.

* * *

"I recognise that look. It is the look that was cemented on my face as a teenager." A woman said as she approached Lucy who was sat in a booth staring at a bottle of beer.

"Lois? What are you doing here?" Lucy asked.

"Helping family." Lois said as she sat down opposite her sister. "So what did he do?"

"Who?"

"The only one who can cause that facial expression. Dad."

"I can't talk about it." Lucy said.

"Then I'll guess. He's arrested Alex, is holding her in unsafe conditions, eavesdropping on confidential conversations with her lawyer, you, is making no effort to find Supergirl and is not let anyone see J'onn."

"How did you-" Lucy started.

"I'm not a Pulitzer prize winner for nothing." Lois shrugged.

"And she had access to my source." Clark pointed out as he sat down next to Lois.

"Your friend, my source." Lois corrected.

"Hi Clark." Lucy greeted.

"Lucy."

"Anyone else joining this discussion?" Lucy asked.

"Just me." James said sitting down next to his former girlfriend. "So how was Alex?"

"She should be in a hospital, not imprisoned in a cell surrounded by aliens who want to kill her. Dad is really making a statement." Lucy explained.

"Did she say anything about Kara?" Clark asked.

"She said she thought Lena Luthor could be involved."

"Any evidence?" Lois asked.

"Not that she told me. But I think she knew that dad was listening to every word so didn't want to give more information."

"What do you think Olsen?" Lois asked. "I mean you dated her."

"She wouldn't." James said.

"You hesitated." Lois pointed out. "You think she could be involved."

"We don't even know what is happening." James argued. "But she's been out of contact for a while. Last time she dropped off the planet she had locked Sam away and was trying to stop Reign."

"Sounds like a big coincidence." Lois said.

"And she offered to sell General Lane Kryptonite." Clark said.

"Not exactly, she said she would consider it when he had paid off the DEO's debts." James clarified.

"Which wasn't a no." Clark pointed out.

"That with the fact she's a Luthor, it's a lead worth chasing. Maybe I'll go visit her." Lois said.

"Or, I'll go visit her." James said. "If she knows something she is more likely to talk to me."

"Fine, but if you don't get anywhere I'll have the next crack." Lois said before looking at Lucy and asking.

"Can you get Alex off?"

"Not easily. Dad is wanting to make an example out of her, which the DEO's lack of rules makes easier for him. And the argument that will almost guarantee she walks she won't make." Lucy said.

"What argument?" Clark asked.

"Saying she tried to bring Jeremiah in, but he attacked her and tried to kill her." Lucy explained.

"She'll never say that." Clark and James said in unison.

"Even if it meant finding Supergirl?" Lois asked.

"Okay, maybe for that." James said.

"Only we don't have that leverage so it wouldn't help. But then again Alex being locked away may not be a bad thing." Lucy said.

"Why?" Lois asked.

"She's still really sick. Locked up she has to rest. Out here she'll push herself too hard." Lucy argued.

"What about J'onn?" Clark asked.

"From what Winn told me there is no change." James explained. "But he is locked down."

"Which is kind of suspicious in itself." Lois said.

"Any theories on what happened?" Clark asked.

"No. But the General is not putting resources into it anymore." James explained.

"I think it is time Superman paid a visit to the DEO." Clark said.

"Why?" Lois asked.

"To visit an old friend and ask General Lane why he is not helping find his cousin."

"I'll talk to Lena." James said.

"We'll go to Alex's place and figure out what she was up to." Lois said.

"We?" Lucy asked.

"You're her lawyer." Lois said. "But a hopeless investigator. Let's go."

-00-

"Lois? Lucy?" Eliza asked when the sisters entered Alex's apartment.

"Eliza? What are you doing here?" Lucy asked. "Sorry, stupid question. When did you get here?"

"About an hour ago. I went to the DEO, but they wouldn't let me in. They wouldn't let me see Alex. Winn said you're her lawyer. Why does she need a lawyer?"

"There is evidence that she has been with Jeremiah. My father has charged her with aiding and abetting an enemy of the state." Lucy explained.

"Jeremiah's involved in all this?" Eliza asked.

"We don't know. Alex hasn't said much?"

"Is she okay?" Eliza asked. "Why was she in hospital? Should she be out of hospital?"

"She had an infected wound. It looked like a stab wound, only it wasn't very deep. Alex hasn't said how it occurred. She was released by the hospital this morning. They wouldn't have released her if they didn't think it was safe to do so." Lucy said.

"But she's okay?" Eliza asked.

"She still needs to rest." Lucy replied.

"What happened in here?" Lois asked looking round seeing the place had been ransacked.

"The DEO, or at least dad's people at the DEO." Lucy said. "After it looked like Alex hadn't left her apartment for two days he sent in a team. Didn't find Alex, but found her phone and her tracker. He had them search the place for an evidence of where she might be."

"But back then he didn't know she had met up with Jeremiah so what right did he have to search the place?" Lois asked.

"Actually he did. He received an email containing a photograph of Alex and Jeremiah." Lucy said.

"From who?"

"Don't know." Lucy said. "And before you ask this place could be bugged."

"I'll save it for later." Lois said.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	11. Chapter 11

**A/N:** Thank you for the comments.

 _Guest_ \- I am picturing a (slightly strange) combination of Margot Kidder (I grew up with the films) and Erica Durance (I only saw a few episodes of Smallville, but she made an impression) combining to be a really good Lois Lane. I don't really watch TV anymore so can't think of anyone who naturally fits that role, if pushed though maybe Saoirse Ronan (great actress in a variety of roles) or Phoebe Waller-Bridge (has the snark down) or perhaps Rachel McAdams...but I am probably completely oblivious of an obvious contender.

Guest(2) - It would be one of the greatest moments of TV realism if in 3 or so years time they bring Max back with the omegahedron weaponised in someway and it turns out he has spent several years taking it from research to weapon rather than the 2 mins shoes normally spend on that stage.

* * *

"Superman. This is a classified facility, and home to an organisation you have chosen not to work for. You shouldn't be here." Lane said when Superman flew into the DEO.

"I won't stay long." Superman said.

"Why are you here?" Lane said.

"Firstly, I want to know how the search for my cousin is progressing."

"It's not. This is not a lost and found department. Your cousin does not even officially work here. My job is not to keep tabs on her."

"Then I'll be staying around longer while I search for her myself." Superman said.

"As long as you don't waste my resources and you leave the DEO you can do as you please. Now, we have work to do so I suggest you leave."

"Not until I've seen J'onn." Superman said.

"He's in quarantine." Lane said.

"I won't be leaving until I've seen him and I doubt you'd be able to stop me, especially as you haven't got your supply of Kryptonite yet."

"Are you threatening me?" Lane asked.

"Just making an observation. Where is J'onn? I won't be leaving until I've seen him." He reiterated.

For a moment Lane stared at the Man of Steel who started back. Eventually Lane said. "Agent Schott, accompany Superman to the Director's room."

"Um, yes Sir." Winn said scampering to his hero's side and saying "This way."

Once they were out if the control room Winn asked. "Did that seem too easy?"

"Yes." Superman said. "Which either means he has nothing to hide or we are walking into a trap."

"I really hope it is the former." Winn said.

"I'm surprised you're still here after everything Lane has done." Superman said as they walked down the corridor.

"I can do more good on this side of the fence." Winn pointed out.

"Have you seen J'onn?" Superman asked.

"No. I'm not allowed anywhere near him."

"When we get in there I need your help." Superman said.

"Of course. Wait, are you breaking him out?"

"No." Superman replied. "But I need a minute alone with him."

-00-

"Where are we?" Eliza asked as Lucy showed her into an office at CatCo.

"It's our former base of operations." James explained. "Winn set it up after Kara came out as Supergirl and before he worked for the DEO. It's where we could help get information on who Kara was fighting."

"Very few people know about it." Lucy said. "But we have swept it and it is safe to talk here."

"Then can someone please tell me what is going on?" Eliza asked. "I mean really going on. What happened to Alex and where is Kara?"

"It's kind of a long story." James said directing Eliza to the couch. Once she had sat down James pulled a chair over and sat opposite her before explaining. "After everything that happened with Sam and Reign as well as Lena, Kara was feeling down so went off for a few days break."

"By herself?" Eliza asked surprised.

"Alex tried to go with her, but she wanted to be alone." James explained. "We think Kara returned when she was meant to as she sent a text to Alex, only she immediately flew off and no one has seen her since. Shortly afterwards General Lane took over the DEO and is watching things really closely."

"What's happened to J'onn?" Eliza asked.

"While Kara was away J'onn was attacked by some energy weapon and has been in a coma ever since." James said.

"What's wrong with him?" Eliza asked.

"We don't know and he's in quarantine so we aren't likely to get answers anytime soon." Lucy said.

"After he took over he banned anyone looking for Supergirl and everyone was monitored. Alex deliberately got suspended so she could go and find Kara but still be able to come back and help J'onn. Only while she was suspended she went completely off grid and someone sent a photo to Lane showing her with Jeremiah. That's when Lane ordered her arrest. For days no one knew where she was until someone brought her into hospital."

"Someone?" Eliza asked.

"A man, we were guessing Jeremiah, but he didn't hang around. She was in and out of consciousness for a couple of days, but eventually the fever broke and she woke up. Only Lane was watching and when she woke she was arrested for aiding and abetting a terrorist and taken to the DEO where she is being held." James summarised.

"But she's okay?" Eliza asked.

"She needs rest. But she seems okay." Lucy assured her.

"And Kara?" Eliza asked.

"No one knows."

"Didn't Alex say anything?" Eliza asked.

"No." Lucy said. "She has barely said anything."

"Well how did she get hurt?"

"I don't know, I'm sorry." Lucy said. "But I think she knew my father was listening in and was being deliberately silent. The only thing she said was she thought Lena was involved."

"I went to see her but can't get hold of her. I'll keep chasing." James said.

"We will figure this out." Clark said entering the room.

"Clark." Eliza smiled before standing and hugging him.

"Eliza." Clark replied returning the hug. "How are you?"

"Scared." She confessed.

"Alex will be okay and we will find Kara." He assured her.

"I wish I had your confidence." Eliza said.

"Did you get to see J'onn?" Lucy asked.

"Yes. Your father didn't appreciate it, but realised he didn't have much choice. Although he still gave in more easily than I was expecting."

"And?" Lois asked.

"Apart from not waking up, he looks fine." Clark said before turning back to Eliza and saying. "I need your help. For that I need to take you away for a few hours, maybe a day." Seeing her hesitation he added. "This is Alex's best chance. Trust me."

-00-

When Kara woke she found herself back on a metallic bed.

"Lena?" Kara asked stumbling off the bed and approaching Lena. Before she reached her former friend though she found herself repelled by an invisible shield. "What's going on?"

"Probably exactly what you think." Lena said. "You are at a secret lab of L-Corp where you are locked away in a Kryptonite cell."

"Why?" Kara asked looking completely broken.

"The answer to that, you really won't like." Lena said walking towards the cell.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	12. Chapter 12

**A/N:** Thank you for the comments.

 _Guest_ \- up until an hour ago my orignal list hel (Saoirse Ronan (although maybe she's a little young) or Phoebe Waller-Bridge or perhaps Rachel McAdams.) But now I thin Rebecca hall. Meta Max would be great.

Whalegang34 - Things should start to make progress soon.

* * *

"Alex." Lucy said entering her cell the next day. "How are you feeling?"

"Bored. Any sign of Supergirl?"

"None." Lucy said. The response causing Alex to frown. "I should warn you that our last meeting was monitored by my father and he is probably doing the same this time. I have lodged a formal complaint, but I don't know when I will get a response."

"I'm sorry you are stuck in the middle." Alex said.

"I'm not in the middle. You are my client." Lucy said. "Remembering what I just told you about this room being monitored, is there anything else you want to tell me?"

"No."

"Well I have something to tell you. I went to your apartment, your mother was there." Lucy said.

"Is she okay?" Alex asked sitting up straighter.

"Worried about you." Lucy said. "Clark and Lois are also in the city. Lois doesn't trust dad so has had your mom moved somewhere safe." She went on half lying to throw her father off, if he was listening. "If I can, is there any message you want me to give her?"

"Just tell her I'm okay." Alex said. "Did you chase up with Lena?" Alex asked.

"We tried, but she is also missing. Well elusive is maybe more accurate. According to her assistant she is on a business trip." The comment causing Alex to loose herself in her own thoughts.

-00-

When Clark and Eliza arrived back at CatCo several hours later Clark said. "I'll find the others and get them here. In the mean time it will be safer for you to not leave this room."

"You make me sound like a prisoner."

"I didn't mean to. I am just trying to keep you safe."

"I know." Eliza said.

"I won't be long." He assured her before leaving the office. Once he was gone Eliza started to pace the office impatiently waiting. After what felt like an eternity she said.

"I'm not wasting any more time." With that she marched out of the office.

-00-

As Lena grabbed a thumb drive from her office safe she heard a commotion outside.

"You can't go in there. I will have to call security." Jess said to the unknown visitor. Moments later the office door opened.

"Dr Danvers." Lena greeted surprised when Eliza entered her office.

"You know who I am?" Eliza asked.

"From the photos in Kara's apartment." Lena explained before looking over to Jess. "It's okay Jess, I have this. You can go."

Reluctantly Jess nodded and left the office shutting the door behind her.

"What are you doing here?" Lena asked.

"I want to know where Kara is."

"Why would I know?"

"The only thing Alex has said about her investigation was your name." Eliza said.

"And because I'm a Luthor you believe I have kidnapped Kara and am in the process of experimenting on her."

"Kara always spoke fondly of you. So no, based on what Kara said about you I don't believe that you are involved. But at the same time you are the only lead I have and I would never forgive myself for not following through."

"I'm late for a meeting." Lena said standing. "Why don't you ride down with me and I'll try to put your mind at ease." She said directing Eliza out of her office.

"Jess, I am going to my meeting at CatCo. I won't be back until tomorrow morning." Lena said to her assistant as she walked towards the elevator.

"Of course." Jess nodded before watching Eliza and Lena enter the elevator. As the doors shut Lena opened a panel and placed her hand on a scanner.

"What's going on?" Eliza asked.

"Are you sure you still trust me?" Lena asked as the elevator plunged downwards. When it finally stopped Lena stood in front of another panel and let her retina be scanned before the doors opened. "This way." She said to a confused Eliza as she led her through a corridor going through several security measures.

When they finally reached another door Lena said.

"What you are about to see is not what it looks like. I'd appreciate you not killing me the second we step into this room."

Confused Eliza silently nodded and watched as Lena opened the door.

-00-

"Lucy, can we talk?" Winn asked when he saw Lucy walk through the DEO.

"Of course." Lucy said.

"We probably want to do this in front of your father."

"You sure?" Lucy asked.

"No." Winn said.

"Why don't we start off with a private conversation and see where it goes?" Lucy suggested.

"Um sure." Winn said as he followed Lucy into a meeting room. "How's Alex?"

"Withdrawn, worried about Supergirl." Lucy explained.

"Right." Winn said.

"So what did you want to talk about?" Lucy prompted.

"What proof does your father actually have against Alex?"

"You know I can't discuss that with you." Lucy said before pausing then adding. "Specifically. In generic terms most of the case in circumstantial, held together by one key piece of evidence."

"And if that evidence was proved to be fabricated the case would fall apart?" Winn asked.

"Possibly. Right now my father seems to be treating this a personal crusade so I would need to take the evidence to a higher level. But in principle yes, it would be enough to get Alex released. Why?"

"Well, say hypothetically I had seen the evidence and could prove it had been fabricated, would that help?"

"You've seen the photo? How? Actually don't tell me. How confident are you that it was fabricated?"

"One hundred percent. The meta data is all over the place. Plus the image of Alex is a definite match of another photo. Some one found the photo and changed it to include Jeremiah."

"Are you sure?"

"Yes."

"And you can prove it?"

"Yes."

"Let's go."

"Where?" Winn asked.

"To see Cat."

"As in Grant? Can't you do that without me?" Winn asked.

"No. Get your evidence and meet me out front in five minutes."

-00-

"You sure you brought her back?" Lois asked when she and Clark entered the empty CatCo office.

"Of course I'm sure." Clark said. "Why would she leave?"

"She probably hates waiting and wanted to help her kids." Lois pointed out.

"I should have waited with her." Clark said as Lois's phone buzzed.

"That was Lucy, she has to go to DC."

"Why?"

"Something about Alex. She says she'll be back as soon as she can." Lois replied.

"Is Alex okay?" Clark asked frowning.

"She doesn't say she isn't. She'd tell us if there was a problem." Lois assured him. "Let's assume Lucy has everything in hand. I suggest you get Jimmy and we start searching for Eliza."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	13. Chapter 13

Stepping into the large room, which looked like a lab, Eliza's eyes were immediately drawn to the middle area, where her adopted daughter lay on bed.

"Kara?" Eliza asked before turning to Lena and asking. "What have-"

"Not enough." Lena replied as Kara saw the new arrivals and sat up.

"Eliza?"

"Kara." Eliza said rushing to the area, only to be repelled.

"There's a forcefield." Lena said.

"Why? What are you doing to her?" Eliza asked.

"She's trying to fix me." Kara said.

"You are not a broken toy." Eliza replied before looking at Lena and demanding. "Let me in."

"Kara?" Lena asked.

"You've secured the lab?" Kara asked.

"Yes." Lena replied.

"Are you sure?" Kara asked.

"Will you two stop and explain what you are talking about." Eliza snapped.

"Cadmus did things to me. It's not always safe to be near me." Kara said before nodding at Lena who lowered the forcefield

"Where have you been?" Eliza asked hugging her. "I've been so worried about you."

"I'm sorry. But I didn't want to endanger you." Kara said hugging her foster mother. "Which is why you need to leave before I do something."

"Kara, I know you. You couldn't hurt me."

"I wish that was true." Kara replied sadly. "But it's not safe for you here. How did you even find me?"

"The only thing that Alex said was she thought Lena was involved in your disappearance."

"You've spoken to Alex? Is she okay?" Kara asked.

"I've not been allowed to see her." Eliza said.

"What do you mean not allowed?" Kara questioned.

"You don't know?" Eliza asked looking from Kara to Lena and back again.

"Know what?" Kara asked.

"Alex has been arrested by Lane."

"For what?" Lena asked before Kara had the chance.

"Aiding and abetting a fugitive." Eliza said. Seeing Kara's confusion she added, "Jeremiah."

"Jeremiah?" Kara asked lost.

"As we can't get to Alex we don't know what happened, unless you know anything?" Eliza asked looking at Lena.

"Not much, all they said was Jeremiah rescued Kara and then Alex joined him before they brought her here." Lena explained.

"He rescued me?" Kara asked confused.

"Apparently." Lena said. "Why do you look doubtful?"

"He was operating on me." Kara said.

"What do you mean?" Eliza asked.

"I mean I remember waking and he was burning my stomach."

"Are you sure you weren't hallucinating?" Lena asked.

"Yes. It was him." Kara said looking lost subconsciously holding her stomach.

"I don't know who did what to you when Cadmus had you but Jeremiah was trying to help you when he was here. He told Alex what work he had done for Cadmus knowing full well Alex might never forgive him."

"How did Alex take it?" Kara asked.

"She was more concerned about you." Lena said. Frowning Kara looked at Eliza and said.

"I am really happy to see you, but it's not safe for you here."

"What are you talking about?" Eliza asked.

"They put things in me." Kara said.

"Things?" Eliza asked.

"It's probably easier to show you." Lena said pulling up some medical images. "We think they put in several small lead encased pellets. Each pellet has a different type of Kryptonite."

"Why?" Eliza asked Lena as she pulled Kara in for another hug.

"Control. My mother wants to prove aliens can't be trusted, to do that she needs a series of demonstrations. Demonstrations that occur when she wants. Some of the pellets have red kryptonite, some silver, some green. Each pellet has a small charge attached which she can remotely detonate. Don't worry, no signals can get in here."

"Why would she do this?" Eliza asked.

"I think she wants to force Kal to kill me, so she can break him." Kara said.

"But we can get the pellets out." Eliza said.

"Unfortunately, each pellet is covered in a stealth material so they are very hard to locate." Lena explained.

"But you did. I can see them on the scans." Eliza said.

"It may not be all of them. When I figured out what had happened I reconfigured the scanner to look for a specific material, there is no guarantee that all the pellets are made from the same material. And that's not the only problem."

"What else?"

"The technology wasn't tested properly and it is malfunctioning. As Kara's powers started to come back her body started fighting the pellets, which has caused some of them to crack and release various types of Kryptonite into Kara."

"Are you okay?" Eliza asked turning her attention back to Kara.

"It's been worse for Lena….I'm really not a nice person."

"You can't help the effects of red kryptonite." Lena replied before looking at Eliza "Fortunately she does not have all her powers and the Kryptonite shields are holding."

"But I can't risk going out there where I may hurt people." Kara said.

"Why can't just remove the pellets?" Eliza asked.

"We can, well I can't. We need Alex or someone with equivalent knowledge of Kara's physiology." Lena said. "We would also need to inject intravenously Kryptonite into Kara. Right now she isn't strong enough."

"Why hide down here? Why not ask for help?" Eliza asked.

"Alex was convinced we couldn't trust Lane. And from what my people are saying Lane is watching Winn and James very closely. Even if he wasn't my mother is keeping a close eye on events and we can't risk her finding Kara. The fewer people who know, the safer Kara is."

"Then why bring me down here?"

"Kara needed a friendly face and I could see how worried you were." Lena explained before looking at Kara. "You need to rest."

-00-

Having ensured Kara had fallen to sleep Eliza approached Lena and on seeing some scans asked.

"Are they Kara's?"

"Yes."

"I recognise that structure. It's the Medusa virus. Is Kara infected?"

"No, not exactly." Lena said glancing back at Kara to ensure she was asleep. "What my mother did to Kara was out of revenge. This," she said pointing at the screen, "is her end game."

"What do you mean?"

"She is trying to make a modified version of the virus that will kill all aliens. But it will be much more deadly than the previous version and not just constrained to Earth. She somehow managed to get hold of Pestilence's virus. She is using that, Medusa and Kara's immunity to make the ultimate bio-weapon. No non-human will be safe. I was hoping I could find a flaw in her work. But so far nothing."

"Perhaps I can help, I have experience with the Medusa virus." Eliza offered.

"It's all yours." Lena said.

"Before I start, I don't even know how to start thanking you, but I need something else."

"What?" Lena asked.

"Can you make this?" Eliza asked passing her a thumb drive.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	14. Chapter 14

**_A/N_ **thanks for the comments. I am jumping timezones at the moment so posting will be at odd times of day...but hopefully it will remain almost daily

 _Guest-_ Thanks, things should start to make more sense from now on...

Guest (2) - Kara and Lena will discuss what happened...not sure about Eliza at the moment. Definitely no plans to bring in ray Palmer (I have only seen him in the crossovers so don't think I could write him). Lillian's insanity has not quite peaked.

* * *

"You going to lie there all day?" Lucy asked as she opened Alex's cell.

"It's not like I can go hiking." Alex said sitting up, grimacing as she moved her side.

"No, but you can go to the infirmary." Lucy said helping Alex to her feet.

"I'm fine." Alex said.

"No you're not. In fact you are so not fine you are starting to show Kara's inability to lie." Lucy said as she helped Alex out of the cell.

"Does your father know I am getting treatment and walking round the DEO?"

"He does." Lucy said. "Do you want me to get a chair?"

"No. I have a reputation to maintain." Alex said. "And it is only eight-three feet away."

"How much time do you spend in the infirmary to know the distance from here?" Lucy asked noticing Alex was putting more of her weight on her.

"It's not my fault I don't have healing powers." Alex said.

-00-

"No sign of the infection coming back." Hamilton said once she had finished the examination. "You just need rest."

"Good thing I am confined to a cell then." Alex said.

"You don't know?" Hamilton asked.

"Know what?" Alex asked.

"You should talk to Major Lane." Hamilton said quickly leaving.

"What's going on?" Alex asked as Lucy stepped into the room.

"What do you mean?" Lucy asked.

"Hamilton was acting weird. What's happened?"

"You have been released."

"I have? You are good."

"It's not me you need to thank. Evidence emerged that proved the photo of you and your father was fabricated."

"Really?" Alex asked confused.

"Yes. So there is no evidence to suggest you ever met your father. So the President ordered your release."

"She did? When?"

"This morning."

"This morning? You didn't feel like mentioning my new found freedom earlier."

"If I had, I didn't think you would have come to the infirmary." Lucy pointed out. "But you are now free to go and I know James wants to catch up with you."

-00-

"You weren't kidding when you said she looked awful." Lois said bluntly when Alex and Lucy entered the office at CatCo.

"Hi Lois." Alex said as she scanned the room and saw Lois, Clark and James. "Where's mom?"

"You didn't tell her?" Lois asked her sister, her tone disapproving.

"I wanted to do that here we could talk freely." Lucy said.

"What's going on? Where's mom?" Alex asked.

"We don't know." Clark said.

"What do you mean you don't know?"

"She went to visit Lena a couple of days ago and no one has seen her since." James explained.

"Have you talked to Lena?"

"She's also missing. They were seen leaving L-Corp together."

"I need a decoy." Alex said.

"A decoy?" Clark asked.

"A distraction so if I am being followed they'll stop."

"You know where Kara is?" Clark asked.

"Yes, she's with Lena."

"Are you sure?" James asked.

"Of course I'm sure, I took her there myself." Alex said confusing everyone.

"Why would you take Kara to Lena?" Clark asked.

"Cadmus did something to her and she was really sick. I couldn't take her to the DEO so I took her to Lena."

"So you telling me you thought Lena was involved was trying to help us find Kara." Lucy said.

"Yeah. But if Kara hasn't emerged yet and Lena is missing it means she's still really sick. I have to get over there."

"I'm coming with you." Everyone said.

"You can't come Clark, there is too much Kryptonite." Alex replied.

"You left Kara with Lena Luthor and Kryptonite?" Clark asked angrily.

"It's a long story, one we don't have time for." Alex said. "I'll explain everything when I get back."

"When we get back." Lucy corrected. "They can be the distraction, but I'm coming with you."

-00-

"You sure this is the place?" Lucy asked as they entered the empty lab.

"Yes. We brought her here. We treated her here. This is where we were when I collapsed." Alex said looking round wondering where Kara was.

"Well Lena could have moved them if she thought it wasn't safe." Lucy said.

"Kara was in no condition to me moved." Alex pointed out.

"Don't do it." Lucy said sternly.

"Don't do what?" Alex asked.

"You brought Kara to Lena because you trusted her. Now you are doubting that decision. Don't. You have good instincts. If Lena moved them it was for a reason." She argued before noting Alex sway. "Should you be up?" She asked hurrying to Alex's side and helping her into a chair.

"I'm okay, just a little weak."

-00-

"Problem?" Eliza asked when she saw Lena frown at a monitor.

"Good news, bad news." Lena said. "The good news is it looks like Alex is free."

"And the bad news?" Eliza asked heading over to the monitor, but the second she saw Alex on the screen she said. "She looks like death, what is she doing up? Where is she anyway?"

"It's another of my labs. It's the one she brought Kara to. She must be looking for her. We can send a message from here." Lena offered.

"No. Alex needs a hospital. She's in no condition to perform surgery." Eliza argued.

"What about Kara?"

"I can remove the pellets."

"You?" Lena asked before apologising. "Sorry, I just don't know much about your background."

"I'm an astrobiologist, with knowledge of Kryptonian physiology. And I did help make the cure for the Medusa virus. While Alex has far better knowledge of Kara, in her current state she won't be much help. We both know the surgery will last for hours. Alex can barely stand for a few minutes."

"Will the two of us be enough?" Lena asked.

"We'll have to be."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	15. Chapter 15

**A/N** thanks for the comments

 _Guest_ by the end of this Lena will have a little more respect for Eliza and her abilities.

* * *

"Have you found her yet?" Alex asked when James and Lucy entered the office at CatCo late the following day.

"No. Sorry." James replied.

"There must be some trace of her." Alex said. "If not her, Lena. What about her secretary?"

"She doesn't know anything. She got an email from Lena a couple of days ago saying she was taking a few personal days and was not to be disturbed."

"I have to get out there." Alex said as Clark and Lois entered the room.

"Absolutely not." Clark said catching Alex's statement.

"You can barely stand." Lucy said. "You should be in hospital. Besides you hiding out here has resulted in dad helping search for her."

"How?"

"He wants to find you and believes Eliza and Kara offer him the best chance of drawing you out. So he has ordered Winn to search for them." Lucy explained.

"That's good, I think." Alex said. "As long as he doesn't actually find them."

"Don't worry, Winn will tell us as soon as he finds anything out." James said.

"What about J'onn?"

"No one has seen him since Superman forced his way in." Lucy said. "Now you are not being held at the DEO I haven't managed to gain access."

"I can go in again." Superman offered. "But I don't know what good it would do."

"So what now?" Lois asked as the door opened and Eliza rushed in.

"Alex, I've been so worried." She said hugging her eldest.

"I'm okay." Alex said. "But where have you been?"

"With your sister."

"You've found her? Is she okay?" Alex asked pulling out of the hug.

"She's getting there." Eliza said. "What about you?" She asked cupping Alex's face and looking closely at her daughter.

"I'll be better when I've seen Kara."

"I think we all would." Clark said.

"I'm sorry, I need you to do something first." Eliza said giving Clark and small container.

-00-

"Alex?" Kara asked when she saw her sister enter the lab.

"Kara, you're okay?" Alex replied moments before Kara charged at her sister and engulfed her in a hug.

"Careful." Alex gasped as Kara squeezed her too tightly.

"Sorry. I've been so worried." Kara said.

"Right back at you." Alex said as she clung to Kara. When she finally pulled away she asked. "How are you feeling?"

"Like I fought Reign while suffering from Argo fever. But I'm pretty sure I look better than you. Should you even be standing?"

"I'm okay." Alex said. "Better now I know you're okay." She then turned to Lena and asked.

"Why did you move?" Alex asked.

"I wasn't sure how safe it was. If Lane was working against Supergirl he may have interrogated you and you were not in a good shape. You could have talked. Also your father knew where we were."

"So?" Alex asked.

"I didn't trust him." Lena said bluntly.

"Why? He saved Kara." Alex said automatically feeling defensive.

"He managed to break into a secret Cadmus facility, one where my mother was experimenting on Kara, meaning security would have been tighter than normal. He freed Kara whilst apparently destroying the facility. And my mother magically survived. There were too many questions to trust him." Lena argued.

"How do you know your mother survived?" Alex asked.

"I went to go and see her. I needed answers and your father wasn't giving us any."

"And you just happened to find her and then she told you everything?" Alex asked suspiciously.

"She has as much faith in me as the rest of the world. She thought I had turned and when I offered to finish her work she told me what I needed to do...or at least she told me enough. My guess is she didn't tell me everything." Lena said. "But as I said it was enough to figure out what had happened to Kara."

"Did she say my father was working for her?"

"She neither confirmed or denied that. She doesn't fully trust me."

"Well, I trust my dad." Alex said.

"I don't and I felt Kara's safety was more important." Lena said.

Feeling the tension grow Eliza asked Kara. "Are you ready to talk about what happened to you?"

"You know what happened to me. You spent hours operating on me to save me." Kara pointed out.

"What do you mean operating?" Alex asked.

"We'll tell you if you sit down." Eliza said.

-00-

As Lena and Eliza briefed Alex on what had happened to Kara, Kara watched as her sister tensed and her heart rate increased. Once they had finished talking Alex sat rigidly in silence.

Eventually Kara squeezed Alex's hand and asked.

"Are you okay?"

"Me? You're the one who should be asking that." Alex said, her body still tense.

"Your heart sounds like it is trying to break a speed record." Kara pointed out.

"Well I'm angry." Alex said as she thought of all the ways she could kill Lillian before turning to her mother. "Why didn't you get me? I could have helped. I've been free for two days."

"You should have been in hospital." Eliza argued.

"We weren't risking you." Kara jumped in. "It was my decision."

"What happened? How did she get to you in the first place?" Alex asked.

"I got home from the Fortress, but it was much later than I had planned, so I sent you a message asking to meet for breakfast."

"I got it." Alex said. "But you didn't respond to any of my replies."

"Well, just after I sent it, I heard a voice. Lillian can send messages to me at a frequency humans can't hear." Kara explained. "She said if I didn't come she'd kill you. But if I did come you'd be safe."

"And you believed her?" Lena asked. As Alex and Kara turned to look at her she said. "Sorry, I'll leave you to it."

"Stay." Kara said. "You should hear this as well."

"So you walked straight into a snake pit, then what?" Alex asked.

"The guards shot me with Kryptonite darts. When I woke I was chained to the ceiling in Kryptonite cell. Lillian would come in goad me a bit and then run some experiments."

"What type of experiments?"

"I don't know. She didn't tell me what they were for." Kara said playing with the cuff of the sweatshirt Lena had lent her. "She'd inject me with stuff."

"What kind of stuff?" Alex pressed holding Kara's hand.

"I don't know. It had Kryptonite in though, I could feel it. I don't know how long it went on for, but then it changed and I found myself strapped to a bed and Lillian was cutting into me. I guess that is when she was putting the pellets in. I don't know how many times she did it...I lost count, it was too hard to focus….Each time I woke up in so much pain. Even fighting Reign I didn't feel that much pain. I'd wake up for moments then pass out again." On hearing her words Alex squeezed Kara's hand tighter as Eliza prompted, knowing Alex needed to hear about Jeremiah's involvement from Kara.

"Tell us everything. Don't hide anything."

Nodding, Kara looked at her lap, unable to face Alex as she told the next part of the story.

"One time I forced my eyes open and Jeremiah was standing above me doing something to my stomach. It hurt so much, I passed out."

"He was cauterising your wound. He was trying to stop the bleeding." Alex said.

"Were you there?" Eliza asked.

"No. He told me." Alex said.

"How did he even find me?" Kara asked, hoping Alex's explanation was true.

"He'd been monitoring the DEO and Cadmus. He left hidden surveillance programmes at both organisations." Alex explained. "When he found out you had been taken he attempted a rescue. He told me he got you out and destroyed the facility. After that he took you to a cave and tried to treat you, but the wound on your stomach was getting worse, so he tried to cauterise it. Which worked until you ran away."

"I thought I was alone." Kara said. "I thought you'd left me."

"You knew I was there?" Alex asked confused.

"I woke up. I heard you and Jeremiah talking. Jeremiah told you to leave me and that you were better together. Then I passed out, when I woke again you had gone."

"We were trying to fix a car so we could get you back to the city." Alex said. "I would never have left you."

"So all of that really happened? I mean the woods?" Kara asked.

"Yes."

"That means….I stabbed you. I'm why you're sick."

"No you're not." Alex said.

"How did you know where to find them?" Eliza asked trying to divert Kara from getting caught up in her own guilt.

"When I was at Kara's apartment an email came through to her phone from Kenny Li."

"Should that mean something?" Lena asked.

"He's a, well he was, a friend. He died." Kara said.

"Murdered." Alex corrected. "But as soon as I saw the sender I guessed it had something to do with Kara. There were clues hidden in the body of the message that let me find the cave dad and Kara were in."

"How did you know the message was from your father?" Eliza asked.

"I didn't. I had no idea until I reached the cave." Alex explained.

"It could have been a trap, you shouldn't have gone." Kara chastised her.

"A little hypocritical coming from you." Alex pointed out. "But there was no way I was going to not help you."

"So what now?" Eliza asked. "Are you ready to go back?"

"No." Alex immediately answered. "Until she is fully recovered she is safer here."

"I'll stay if you see a doctor said." Kara said.

"It's not a negotiation." Alex warned.

"You're right it's not." Eliza said. "Kara will stay here and I'm taking you to a doctor."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	16. Chapter 16

**A/N:** Thanks for the comments

 _guest:_ yes and no. Lillian will be back soon.

 _alliedstatis_ \- poor Eliza will need to keep bringing out that power.

* * *

As Lena looked at her computer screen Kara looked at her friend trying to work out what to do. Getting frustrated she started to walk towards Lena.

"Should you be up?" Lena asked.

"I'm fine." Kara said.

"You've just had major surgery, which involved Kryptonite being pumped through your veins." Lena pointed out.

"But now I am free from Kryptonite I've healed." Kara countered.

"Physically maybe." Lena said. "Besides if Alex comes back and you are not resting I'll be the one who pays the price."

"I wanted to say thank you for everything you did."

"You're welcome." Lena said as she continued to work. When Kara hovered behind her she asked. "Something else?"

"Can we talk?" Kara asked.

"Isn't that what we're doing?" Lena responded.

"I mean really talk." Kara said causing Lena to face her.

"Recently that has resulted in us fighting." Lena pointed out.

"I'll take the risk." Kara said before saying. "I'm sorry."

"For what?"

"I said some awful things to you."

"You were under the influence of Red Kryptonite." Lena reminded her. "You weren't in control."

"I still said it. All I seem to have done recently is hurt you." She said sadly. "My life on Earth has been about keeping secrets. If it were just me I wouldn't have, but I could never endanger my cousin or Alex."

"I know. And I don't object to you having secrets because I know if you have them they are for a good reason. What I object to is the assumption that you have the right to know everyone else's." Lena said.

"On Krypton I thought there were no secrets in my family." Kara said. "I know I was just a kid, but I truly believed I knew everything about my family. Then everything unravelled so quickly. I discovered that Alex was secretly working for the DEO, an organisation that had Kryptonite, J'onn was a Martian, my aunt was alive and had been sent to Fort Rozz by my mother, who had used me as bait to catch Aunt Astra." Kara explained.

"Then Alex killed your aunt and lied about it." Lena said. Seeing Kara's surprised look she explained. "Alex told me."

"It wasn't just Alex who lied, it was Winn about Siobhan and James about Guardian as well. And then I found out other things about my parents. I just wanted to go back to when I could believe in everyone." Kara said. "And I thought I had that with you. And I know it is hypocritical as I was lying about who I was, but I thought you were my first friend who didn't lie to me. Then I found out about Sam and at first I was angry about the fact you had hidden it, but your reasons made sense, but they made me think that you didn't tell me because you didn't trust me or because I was not a good enough friend."

"What are you talking about?" Lena asked.

"Growing up Alex and I would stay up to all hours sharing. But it turned out we weren't sharing. I was telling Alex all my problems and I never gave Alex time to focus on herself….I never allowed her to worry about herself. If I had she would have figured out who she was earlier, she could have found happiness sooner. I was such a bad sister and I tried to be a better sister and a better friend. But when I found out you were keeping things I started to think it was because I was a bad friend and I hated myself for it."

"You weren't a bad friend." Lena said. "You were there for me and you believed in me." She added before recalling. "You looked so disappointed in me when you found out I had Kryptonite. I was so glad I was telling Supergirl you rather than Kara you though."

"Why?" Kara asked confused.

"Kara Danvers was my friend. Supergirl wasn't."

"We're the same."

"No...no you're not. Kara lets me be myself, she doesn't mind my flaws. She supports me, puts up with me and my pity parties, makes me feel normal. But Supergirl...Supergirl expects more from me than I have to give. I feel like I am being judged and I can't win."

"I never judged you." Kara said. "I'm sorry it felt that way. I just wanted the world to see you as I did."

"The world's view will never change." Lena said before the two fell silent. Eventually Kara said.

"I'm going to put an end to Cadmus."

"And you want my help?" Lena guessed.

"No...well yes...but no. I can't ask you do this..It would be asking you to betray your mother."

"If you don't want my help why tell me?"

"I'm tired of hiding things." Kara replied sadly.

"If you really are trying to stop Cadmus you need my help." Lena said.

"No. I'm not putting you in danger." Kara said.

"Regardless, right now you couldn't fight your way out of a paper bag. I suggest you get some rest." She said standing. "Will you be okay alone?"

"Sure. Where are you going?"

"I do have two businesses to run." Lena pointed out. "I won't be long. The door is set up to only open for me, Alex or Eliza. You'll be safe." With that she took the thumb drive out of the computer and said. "Don't worry, I'll bring back potstickers."

-00-

As they drove through the streets Alex said. "You should have told me what you were planning. I should have been there. I could have helped."

"You were barely able to stand. There was no way you could have done the surgery." Eliza reminded her as free from the dampener at L-Corp her phone started to buzz.

Picking up her mother's phone Alex read the screen and said. "Lucy is looking for us. She wants us at the DEO."

"Are you getting arrested again?" Eliza asked.

"I hope not." Alex said responding to the message as Eliza drove towards the DEO. "You should have told me." Alex repeated.

"And you should have told me Kara was missing." Eliza countered. "But right now you need to focus on you. You shouldn't be up."

"I'm okay." Alex said.

"No you're not." Eliza said.

Instead of answering Alex sighed and looked out of the window.

"How was he?" Eliza finally asked.

"Okay." Alex said, guessing Eliza was talking about Jeremiah. Before Eliza could respond her phone buzzed again and Alex once again read the message.

"Lucy said it is good news."

"Makes a change." Eliza commented. "Ask her to have Hamilton get ready."

"For what?" Alex asked.

"You." Eliza replied. "No matter what Lucy wants you are not doing anything until you see a doctor and Hamilton is as good any."

-00-

"Welcome back." Lucy said as they walked towards the control room.

"I hear you've been making more trouble than normal." J'onn said.

"J'onn? You're okay?" Alex asked.

"Thanks to your mother." He explained.

"Superman obtained some blood samples and scans during his first visit. When he took me to his Fortress I was able to figure out what was wrong with him and then when i was at Lena's lab we made made a cure." Eliza said. "I'm just glad it worked."

"How are you?" J'onn asked having already seen Alex's medical report.

"I'll be okay." Alex said.

"You have a lot to catch me up on." J'onn commented.

"I do." Alex said.

"But not yet. You are going to the infirmary." Eliza said.

"I need to brief J'onn." Alex argued.

"No, you need to recover." Eliza said.

"Your mother's right." J'onn said. "We'll talk after Hamilton has seen you."

"Fine." Alex sighed. "But first I need to say hello to Winn."

Not waiting for the arguments she approach the technician.

"Winn."

"Alex! Hey, how are you?"

"I'm okay." Alex said. "I hear I have you to thank for me getting released."

"It was nothing."

"No it wasn't." Alex said. "Especially as I saw the photo and know full well it wasn't fabricated."

"I don't know what you're talking about." Winn said looking guilty.

"I don't know how you did it, but thank you." Alex repeated before walking off.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	17. Chapter 17

**A/N:** Thanks for the comments

 _guest:_ Winn is definitely one of the under appreciated _characters._ Regarding Lane, yes no one at the DEO has anything good to say about him, but I am still undecided on an aspect so no big showdown for now. Thanks for the additional info regarding your plot idea _._

* * *

"Lena, I heard you changed sides again." Lillian commented.

"You heard wrong. Or right. Depending who you heard it from. Who did you hear it from?" Lena asked.

"I have several sources." Lillian said.

"I'm sure." Lena nodded. "But regardless of who they were I'm sure you've realised there was a change of plan. You experiment was too unstable and several of the pellets broke. Assuming you didn't want Supergirl to die before you had her carry out your plan I was forced to change the plan and remove the pellets containing the green, silver and red Kryptonite. Your other ones, the ones you didn't tell me about, are still there though."

"You found them?" Lillian asked surprised.

"It wasn't that hard. Having examined the pellets in more detail I realised you were using a very specific frequency to send the commands. All I had to do was create a low power signal at that frequency and monitor Supergirl's body. Unsurprisingly the pellets you hadn't told me about started to radiate a reply. I could use that to find them. I will hand it to you, hiding one in the liver was clever. Not only as you knew the liver would heal so quickly and trace of what you did would disappear, but also the placement of the pellet meant that the Kryptonite would go unfiltered into her blood."

"I really do underestimate you." Lillian said.

"And not trust me apparently."

"Do you blame me?" Lillian asked. "You have a history of turning your back on your family."

"So what was so special about those pellets?"

"You don't know?" Lillian asked.

"As I said, I left the pellets in her so you can do what you please, but I think I deserve to know what your plan is? At the very least so I can come up with suitable denial of involvement."

"You always knew how to protect yourself." Lillian commented.

"I learned from you. So what's in the pellets?"

"Kryptonite." Lillian said.

"I guessed that much. What type? Red, Silver, Green?"

"None of the above. It's a special formula we worked on. Obviously it has never been tested but one of them contains a version, which we believe will turn Kara evil. She will make the worldkillers look like innocent girl scouts. If it works like it is meant to she will kill indiscriminately. There will be only one person on this planet capable of stopping her."

"Superman." Lena said. "But last time they fought Supergirl beat him, won't she do that again?"

"That is where the second pellet comes in." Lillian said. "It is weakened form of green Kryptonite. It will weaken her enough to give Superman the advantage. But not enough to mean he won't have to kill her. It is the perfect plan. Supergirl is shown to be evil. Superman is forced to kill her, something that will break him. The people will fear these god-like aliens so when they all start dying from a mystery illness no one will kill. The Earth will be protected."

"Speaking of protection, what is happening with the virus? Are you sure humans are safe?"

"Quite sure." Lillian said. "You will see for yourself when we have dealt with the Kryptonians. Where is she?"

"Telling you wouldn't help your cause. You need her to come to you." Lena pointed out. "Something I am sure I can arrange."

-00-

"Okay I have swept the room and it is safe to talk." Winn said two hours later when the group assembled in the briefing room.

"Where's General Lane?" Eliza asked.

"Gone back to his command." J'onn replied. "For now, it's just us." He then turned to Winn and asked. "Are you sure it's safe to talk?"

"I'm sure." Winn confirmed.

"How's Kara?" Lucy asked.

"Ignoring the major surgery, she's fine." Alex said bitterly.

"Surgery?" Superman asked.

"I'll catch you up on everything." Eliza assured him. "But the important thing is she is safe and recovering."

"Where is she now?" Superman pressed.

"At Lena's lab, resting." Eliza said.

"She is still weak." Alex added.

"Are you sure you can trust Lena?" Superman asked.

"She's not her brother." Alex pointed out.

"Lena helped treat Kara and she found out what Lillian's plan is and we have to focus our efforts on stopping it." Eliza added.

"Didn't you do that already when you removed the pellets?" Alex asked confused.

"That was just to get revenge on Clark." Eliza said. "Her actual plan is far more deadly."

-00-

"Potstickers as promised." Lena said when she returned to the lab.

"Thank you." Kara said.

"That was less enthusiastic than I was expecting."

"Sorry." Kara said. "I just haven't had much of an appetite recently."

"I'm not surprised after what you went through." Lena said.

"It's in the past now." Kara replied before asking. "Do you know how to find Lillian?"

"You already know the answer to that."

"Will you tell me where she is?"

"And if I do what will you do?" Lena asked.

"Stop her."

"How. You are not recovered and she has Kryptonite."

"She doesn't know I'm better. She'll think she can control me and you could make a device so I know she is trying to activate the pellets so I can make her think she is in control."

"I thought you weren't going to ask for my help."

"Is that a no?" Kara asked.

"You should wait until you are better. At the very least until Alex is recovered."

"Alex can't be part of this." Kara said.

"Why?"

"If she sees your mother she will kill her."

"And you want to save my mother?"

"No, I want to save Alex." Kara explained.

"What about me? If I help you Alex will kill me."

"No she won't. Well maybe she would, but unintentionally you are in danger anyway. If you don't help she'll blame you more than if you do." Kara said.

"Fine, but if you are going to do this you need a better plan than the one you are thinking of."

"You don't know my plan." Kara said.

"No, but I know you." Lena countered. "Your jump first ask questions later approach won't work against my mother."

-00-

"How are you feeling?" Eliza asked as she approached J'onn.

"Pretty good for someone who has been in a coma." J'onn said. "Thank you for everything."

"I didn't do much." Eliza said. "Have any of your people figured out who was behind it?"

"Nothing conclusive." J'onn said.

"If it wasn't tied to Cadmus you are still in danger." Eliza pointed out.

"Right now stopping Lillian my priority. If Cadmus weren't responsible I'll figure out who was later." J'onn replied. "Any luck with the virus."

"No." Eliza said. "But my bigger concern is that Lillian doesn't know what she is doing. One mistake and everyone on this planet will be killed."

"She may be evil, but she is not insane." J'onn said.

"I hope you're right." Eliza replied.

"Where's Alex?" J'onn asked.

"Sleeping." Eliza said. "She's in worse shape than she is willing to admit to."

"She's tough, she'll be okay." J'onn assured her as Superman rushed into the room.

"Problem?" J'onn asked.

"I went to the lab to see Kara." Superman explained. "She and Lena have gone."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	18. Chapter 18

"Supergirl. What a surprise." Lillian said. "Well actually it isn't. I was expecting you." She added as Supergirl walked towards her.

"It's over. You've failed." Supergirl said.

"Have I?" Lillian asked. "That seems a rather ill-informed statement. Even for you."

"Yet here I am." Supergirl said.

"Indeed you are. You are just where I want you."

"Where you want?" Kara asked incredulously.

"Indeed. I planned this with Lena. I thought she would find it harder to get you here, but apparently you really are that stupid."

"Lena is not on your side." Kara said.

"Isn't she?" Lillian asked. "Did she tell you about all our meetings? About the little presents I left in you that she didn't remove? The virus that I will release after you are gone. A virus that you helped create."

"What virus?" Kara asked.

"As I said you needn't worry about it as you will be dead. Which is just as well as otherwise we'd have to add it to your list of failures. And well it is already a big list isn't it?" Lillian said smiling at Kara.

"My failures? You are the one who has always failed." Supergirl said trying to regain the upper hand.

"On the contrary, I normally succeed." Lillian said. "And I learn from my mistakes, which is why I am about to destroy you, your cousin and every other abhorrent alien. Where as you, you are one failure after another. I am amazed you can actually get out of bed in the morning." Lillian went on. "Perhaps it is because you have the memory of a goldfish. Let me remind you. Ignoring all your other recent failures, including misjudging Lena, let's look at why you were sent to Earth. You were sent as a bodyguard for your cousin. But you came late to the party, you failed before you even arrived. To think the man of steel's family thought so little of him that he required a pre-teen bodyguard. He must have been so ashamed and embarrassed when you arrived and told him of your mission. I bet that is why he sent you away." She mused. "But I digress, the point is you couldn't do what your parents wanted and now you will actually cause his destruction. I don't know how this will turn out. One of two things will happen. Either you will kill him, or he will kill you. I had planned on keeping you weak enough that he would kill you. Unfortunately that plan disappeared with the Kryptonite pellets. But don't worry I always get my way. Breaking you will be almost as easy as breaking your cousin."

"You're fighting this crusade alone." Supergirl said.

"Not alone. But I do not depend on anyone. Nor do I have a problem with sacrifices." Lillian said as she pressed a button causing a screen to switch on. Turning to face the screen Kara saw Lena sitting in a room, cuffed to a chair.

"What have you done to her?" Kara asked.

"Nothing much. She is just enjoying my hospitality." Lillian said.

"You said she was part of your plan, that she was working with you."

"I did and I hoped she was, but Lena isn't really a Luthor. She has no loyalty. I can't trust her. Proven by the fact that me men just found her snooping. And regardless of what side she is really on her death will cause you pain."

"Her death?" Supergirl asked.

"In two minutes the room she is in will fill with cyanide gas, ten seconds later she'll be dead."

"You're a monster." Supergirl said.

"No, just pragmatic." Lillian said. "I am not completely heartless, I am telling you so you can rescue her... but there is a catch. The room is filled with Kryptonite vapour. You go in you'll die. Your choice Supergirl." Lillian said. "You can stop me now, once and for all or you can try to rescue Lena, dying in the process. Which is it to be?"

"Where is she?" Supergirl asked.

"Down the corridor, fourth door on the right….oh and there is now sixty seconds until the cyanide is released." Lillian said. Before she had even finished Supergirl disappeared in a blur causing Lillian to say. "So predictable."

-00-

"You okay?" J'onn asked joining Eliza, who stood on the balcony holding a tablet.

"I would be if my daughters stopped trying to give me heart failure." Eliza said. "Any sign of Kara?"

"Winn is working on it. Does Alex know yet?"

"No. She's still sleeping. When she finds out she'll do something stupid." Eliza said.

"Don't worry, there are plenty of people around to stop her." J'onn assured her as Eliza's tablet started to bleep. "Problem?" J'onn asked.

"No. Good news for a change." Eliza said. "It looks like the antidote works. All we need now is to make it."

"Fortunately we know a good lab." J'onn said. "And seeing Lena has disappeared with Kara, there is no one around to object to us using it."

"J'onn!" Winn said hurrying onto the balcony. "I've found her."

-00-

The second Kara had broken into the room she felt the Kryptonite weaken her. Fighting through it she stumbled to Lena who was cuffed to a chair and tried to rip the cuff off her. Weakened by the Kryptonite though she could only strain the metal links, not break them.

"Go." Lena instructed.

Shaking her head Kara tried to summon what strength she had left and focused her heat vision on the metal chain. As the metal melted Lena tugged and the cuffs broke. As Lena got her feet Kara sank to her knees.

"No you don't." Lena said taking hold of her friend. "You need to help me get you out of here."

"Have...go." Kara wheezed.

"Yes, you do."

"No….you….cya...nide." Kara explained as Lena dragged her towards the exit.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	19. Chapter 19

**A/N:** Thanks for the comments

 _Guest:_ Personally I don't see either of those happening. Alura dying I could see as a possibility, but not Kara. Selena killing Ruby I also see (I'm not reading anything into the casting as for the last couple of seasons there have been big changes after the casting announcements). Sam I really hope they don't kill but it is looking inevitable.

* * *

"Kara?" Alex said squeezing her hand.

"Al...Alex?" Kara asked hoarsely as she tried to open her eyes.

"Right here." Alex said. "How are you feeling?"

"Like I've had a night with Aldebaran rum." Kara said before she remembered what had happened. "Lena?"

"She's okay." Alex said. "Right now you need to focus on you. Inhaling Kryptonite vapour is right up there with your dumb ideas."

"But Lena's okay?" Kara said coughing.

"She is." Alex said handing her some water.

"Lillian?" Kara asked after taking a sip.

"Escaped." Alex said.

"Sorry." Kara mumbled.

"Looking like a kicked puppy isn't going to get you off the hook." Alex said as Kara lay back down. "When you have recovered we are having a long conversation about stupidity."

"Yours or mine?" Kara asked as sleep started to take hold again.

"Don't get cute." Alex warned as Kara drifted off to sleep.

-00-

"How is she?" Lena asked when she saw Alex approach.

"Alive." Alex said glaring at the Luthor.

"I told her not to go after my mother." Lena protested for what felt like the hundredth time.

"Then you helped her."

"You would have preferred I let her go by herself?"

"I would have preferred you stopped her or at the very least told us."

"So you could charge in and get yourself killed?" Lena asked. "Kara didn't want you to be involved."

"Not taking Alex was the right choice." J'onn said walking over. "Taking Kara, the wrong choice."

"We should have been told." Alex repeated before looking at J'onn and saying. "You should have told me they were missing."

"There was nothing you could do. We had it covered." J'onn said.

"Covered? Kara nearly died." Alex said before turning in Lena again. "What exactly was your plan, let Kara walk head first into a trap, again?"

"Kara was trying to distract my mother so I could access the database." Lena said.

"And did you?" J'onn asked.

"I did. Which triggered an alarm."

"So she nearly died for nothing?" Alex asked.

"Alex, I know you are angry at me for not telling you." J'onn started. "But Lena has lost a lot too.

I doubt her involvement is going to help her relationship with her mother." He then turned to face Lena and warned. "She'll be out to get you."

"Seeing she just tried to kill me I got that message." Lena said bitterly. "But there is always someone out there wanting to destroy a Luthor."

"I doubt the threat will be constrained to you. She may use you to get to Kara. She knows if something happens to you Kara will feel responsible." J'onn said.

"I know." Lena replied.

"And she'll feel responsible regardless of whether or not you're friends." Alex said. "So if you were thinking of distancing yourself to protect her, it won't work."

"I thought you wanted me as far from Kara as possible." Lena said.

"I want Kara to be happy. Despite your insanely bad choices and poor judgement, Kara values your friendship."

"And that means I should forget everything that has happened and be friends with her?" Lena asked.

"It means you should think about it before you turn your back on her forever." Alex said. "Especially as she nearly died trying to rescue you."

"Kara won't give up." J'onn added. "Trust me. Besides it beats being alone."

"As much as I appreciate everyone having an opinion on my choice of friends, perhaps we should be more focused on stopping my mother."

"Do you think she still believes the pellets are in Kara?" J'onn asked.

"Two of them yes."

"Why two?" Alex asked.

"I told her." Lena replied.

"But why two?" Alex pressed.

"When we were removing them, two were much more inaccessible than the others."

"Mom told me. She also said they had a different type of Kryptonite in."

"They did. I was hoping my mother would explain what type of Kryptonite. So I told her that those two pellets were still in Kara."

"And?" Alex pressed impatiently.

"One was designed to turn her evil, the other to weaken her. She wanted her to face off against Superman who would be forced to kill her. But that is just a side show. Her main goal is the release of the virus."

"I disagree." J'onn said. "Whilst the virus may be the ultimate goal, her plan for Supergirl and Superman is more than a side show. If the world sees Supergirl turn evil fear will spread. Humans will turn on aliens so when the virus hits no one is motivated to help." He said before pausing and then asking. "Do you really think you mother believes the pellets are still in play?"

"Yes. But even if they weren't she knows how to make all the Kryptonite."

"If she thinks the pellets are still in play it may buy us some time." J'onn mused.

"We'll need more than time." Lena said.

"I have a plan." J'onn said. "But I'll need your help. And before you ask I can't afford to pay what you asked off Lane."

-00-

"You okay?" Lois asked as she approached Superman.

"No. I can't help but feel this is my fault. If I handled things differently with Lex, Lillian would not be on this vendetta. Kara wouldn't have got hurt."

"Lex is a psycho." Lois said. "Kara can take care of herself. Besides wasn't she sent here to babysit you?"

"You are worse than Kara is at bringing that up." Clark complained.

"Can you blame me?" Lois grinned before asking. "Is that all that's bothering you?"

"That means you think something else should be." Clark replied.

"You are about to team up with a Luthor."

"Adopted Luthor. And Lena is, well was, Kara's friend. I trust Kara's judgement."

-00-

As Lena approached Kara's room she heard shouting from inside. Increasing her pace she turned the corner, but came to a stop when she saw Alex standing outside the room looking like she was almost smiling.

"What's going on?" Lena asked.

"Mom is yelling at Kara for running off and facing Lillian alone." Alex explained.

"And what are you doing?" Lena asked.

"Enjoying the moment. Growing up mom never told Kara off."

"Because Kara never did anything wrong?"

"No. because as her big sister I should have stopped her." Alex replied. "It was always my fault. As this will be. But for the next minute or so I will enjoy not being in trouble."

"What happens in a minute?"

"Mom will come out and blame us, then yell at us."

"Me?"

"You were responsible." Alex said.

"Whilst I accept a level of blame, why would your mother yell at me?" Lena asked as Eliza exited the room and came to stop in front of them. Closing her eyes Alex waited for the inevitable.

"What were you thinking?" Eliza asked. Opening her eyes Alex was about to respond only to notice Eliza was staring straight at Lena.

"Going was her choice." Lena asked. "I thought going with her was better than her going alone."

"You should have stopped her." Eliza said.

"How?"

"You're smart you should have figured it out." Eliza said before looking at Alex.

"Why aren't you in bed?"

"I'm fine." Alex started only for Eliza to glare at her. Realising she wasn't going to win Alex sighed and said. "I was going to sit with Kara."

"Make sure you both sleep." Eliza warned before marching off.

"That brought back memories." Lena mused.

"Tell me about it." Alex said as she entered Kara's room.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	20. Chapter 20

**A/N:** Thanks for the comments

 _Guest:_ Sacking J'onn now seems a little harsh as he's screwed up big plenty of times before, not to mention lied about who he was. I assume My'rann will die at the end of the season so I could see J'onn taking a little time off to recover allowing someone else to temporarily take charge. The public forgave Supergirl after the Red-K in season one and seeing Kryptonians will beat Kryptonians it would seem like a weak plot to have them turn so quickly on Supergirl...but Edge (if he is still around) could spend the first half of next season using the attack to help gain revenge on Supergirl.

* * *

"Eliza's mad at me." Kara said when she woke and saw Alex.

"So am I." Alex said. "But mom being mad at you should tell you how stupid you were."

"I wanted to stop Lillian."

"Which you didn't. You risked yourself for nothing." Alex said.

"I wanted to protect you."

"My job is to protect you." Alex reminded her. "Not that I've been much good at it recently."

"What are you talking about?" Kara asked.

"You end up in this infirmary way too much." Alex reminded her.

"So do you." Kara countered. "We should make more of an effort not to end up here."

"We should." Alex agreed. "But for now here is the best place for you. Get some rest."

"Alex?"

"Yeah."

"I'm sorry." Kara said. Before Alex could ask her for what Winn entered saying.

"They're ready."

"For what?" Kara asked.

"Nothing. Get some sleep." Alex said leaving the room with Winn.

-00-

"Are you sure you have everything you need?" Alex asked as she met up with Eliza and Lena in the control room.

"We are." Eliza said.

"Well I'm sending a DEO team with you. They'll keep you safe."

"We'll be fine." Eliza said before hugging Alex. "We'll be back as soon as we can. Don't leave this building and look after your sister."

As Eliza and Lena left Alex turned and saw Winn smirking.

"What?" She demanded.

"Nothing. It's just that was nice. A nice mother daughter moment. No yelling, no calling you Alexandra, but yet you being compliant and I am shutting up now."

"Is the building secure?" Alex asked glaring at Winn.

"It is. All electronic surveillance aids have been removed and I am running jammers, just in case." Winn said.

"And the chosen site?"

"Prepped and ready to go. As soon as whoever is in charge gives the signal we'll set off the explosion. Just out of interest who is in charge?"

"Alex." Lucy immediately said.

"I am?" Alex asked surprised.

"Unless you can't handle it." Lucy challenged.

"I just didn't think you'd want me in charge." Alex said.

"I don't work for the DEO." Lucy reminded her. "And I'm guessing you don't want my dad back?"

"God no." Lois commented from the side, before having a dig at Lucy by saying. "And don't forget when this goes wrong it will be a blot on her service record."

"That's not why I'm doing this." Lucy protested. "The team here trust Alex, more importanlty so does J'onn. Alex is in charge."

Nodding Alex turned to Winn and ordered.

"Set off the explosion."

"Done." He said, watching a screen before adding. "And CatCo is reporting it now. Supergirl will arrive on scene in two minutes, around the same time as the CatCo helicopter."

"Let's hope Lillian is watching." Alex commented.

"I will be sending social media into overdrive with this." Winn said. "If she is on Twitter, has a TV or a radio she'll know." He said typing away. "The CatCo chopper is arriving. Channel nine is showing the footage and in comes Supergirl. I could so be a movie director." He added as Supergirl landed in front of the building and blew over it. Seconds later the fire went out.

"How did J'onn do that?" Lois asked. "I mean he doesn't have freeze breath."

"But it looked like it didn't it?" Winn asked proudly. "I've always wanted to do special effects and now I have. Simple pyrotechnics and a little physics and it looks like Supergirl's freeze breath is working normally."

"Concentrate on your job." Alex reminded him. "We can't afford a delay."

"Right, sorry." Winn said. "All signal monitors are operational and nothing...no wait….now." He said hitting a button. Moments later they watched as Supergirl clutched her side and doubled over as if in pain. Moments later she stood, eyes glowing red and walked towards a street sign which she ripped from the ground and swung at cars.

"It makes you wonder what teenage J'onn was like." Winn commented.

"Signal Hughes." Alex ordered. Having done as instructed Winn watched a 'bystander' wonder into the camera shot and start to take a selfie, just before Supergirl attacked them.

"Out of interest does J'onn like Hughes?" Lois asked.

"Feels he doesn't train enough. That's why he was selected for this." Alex said. "Training by demonstration."

"And I thought dad's methods were tough." Lois said as Hughes landed in a heap.

"When are you sending in Superman?" Lucy asked.

"Not for another minute." Alex said before explaining. "J'onn's right, Hughes needs to learn."

"Does Kara go through this type of training?" Lois asked.

"We all do." Alex replied. "That's why Supergirl kicked Superman's ass last year." She added before telling Winn. "Send in Superman."

"Done."

"Have you tracked the signal yet?" Alex asked.

"No. The algorithm is still running." Winn said as they saw Superman land in front of Supergirl moments before they started fighting.

"I thought they had resolved their issues." Winn said getting distracted by the fight on the screen.

"They do know this is just for show right?" Alex asked as she watched the two Supers slug it out.

"It was J'onn's plan." Lucy reminded her.

"Yeah, but they're really going for it." Lois commented as she watched the screen. "Even I am convinced it looks real."

"Like really real." Winn agreed.

"Winn, aren't you meant to be tracing a signal?" Lucy asked.

"Right, sorry. On it." He said as Kara entered the control room.

"What's going on?" She asked looking at the screen.

"Kara? You are meant to be in the infirmary." Alex said.

"Right back at you." Kara shot back. "What's happening?"

"Lillian sent the signal to release the Kryptonite that turns you evil." Alex explained.

"But I'm here, not evil. How am I there, attacking Kal?" Kara said confused as Lucy wheeled a chair over for Kara to sit in before she collapsed.

"J'onn is pretending to be you. As soon as we detected the signal meant to activate the pellet we told him to let rip. Which he did. Then your cousin arrived and tried to stop him. And now they are working through their issues." Alex explained.

"Kal shouldn't be out there. What if Lillian has more crazy Kryptonite?" Kara asked, wincing as Kal crashed into a wall.

"Then J'onn will continue to kick his ass." Alex replied.

"My guy will pull this back." Lois said.

"I have the signal origin." Winn interrupted.

"Send in the strike team." Alex ordered. "Tell Lena and mom."

"On it." Winn said as his eyes were drawn back to the screen.

"When is your guy pulling it back?" Lucy asked Lois as Superman was sent flying again.

"Is no one here rooting for him?" Lois asked.

"Just his biggest fanboy, Winn." Alex said watching the fight unfold.

"Lena says she's ready. Do you want her to release it?" Winn asked ignoring the comment.

"No. Not until we have to." Alex said staring at the screen. "How long until the strike team arrives?"

"Three minutes." Winn said.

"Make sure Vasquez immediately downloads the contents of the database." Alex said.

"Assuming they are going to the right place." Lois pointed out as she glanced at her phone.

"Somewhere you need to be?" Lucy asked her.

"No, just keeping tabs on dad."

"You're tracking him?" Lucy asked.

"Of course I am, he could be involved in this." Lois said. "Don't look at me like that, if this technology existed when we were growing up he would have used it against me."

"You needed tracking." Lucy muttered as Winn announced.

"Strike team going in."

"Any sign of a second signal?" Alex asked.

"No. It looks like Lillian wants Supergirl to kill Superman." Winn said.

"Any sign of Kryptonite signatures?" Kara asked.

"Absolutely none. We chose the location so Lillian wouldn't have had time to deploy any." Winn explained as two Supers continued to slug it out.

"Are we sure J'onn hasn't been effected?" Lois asked. "I mean it wasn't that long ago he was attacked by something that sent him into a coma. Could this be the reverse?"

"No, his attacks are controlled and textbook." Alex said watching the screen. "J'onn is in control. This is all part of the plan." She said before adding quietly. "I hope."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	21. Chapter 21

**A/N:** Thanks for the comments

Alliedstasis _:_ Thanks! I find writing the dialogue much easier than describing action scenes so I'm glad you enjoy it.

 _Guest:_ It depends what actually happens with the Kryptonian trio but if they sacked J'onn for what is about to happen I think it would feel like it would just be continuing this season's depressing theme of creating drama for the sake of it. If the public didn't turn against all aliens after the Daxamite invasion I'd hope they'd show the same maturity this time round especially as turning against the people who are powerful enough to kill you is really dumb and despite everything that happens in the world there must be some non-dumb humans out there...now turning on Ruby (as the offspring of evil) and forcing her into hiding I would get. The reason I mentioned Edge was his character seemed completely wasted, like they had a plan then forgot about it, which makes me thing there really is a plan, if that makes sense.

* * *

"J'onn is really good at being me." Kara commented watching the fight. "Why don't I take more time off?"

"You need money to feed your potsticker addiction." Alex pointed out before looking at Winn. "Anything?"

"The site is definitely a Cadmus base and Vasquez has gained access to the database. No sign of Lillian yet or a potential dispersal device."

"Make sure the site is locked down. I do not want her escaping again." Alex ordered.

"On it." Winn replied as he radioed through the message before turning to Alex and giving her a radio. "It's Vasquez. She says it's urgent."

Taking the radio Alex stepped away from the others to hear the message as Kara asked.

"Are you sure there's no Kryptonite near Kal?"

"I'm sure." Winn assured her as Alex hurried back over.

"Send reinforcements to L-Corp then get me the team at L-Corp on the radio." She barked.

"Done and done. They're on speaker." Winn said.

"Barnett." Alex started.

"Yes ma'am."

"Lockdown the lab. An attack is imminent."

"Yes ma'am." He said.

"Reinforcements are on their way." She said.

"What's going on?" Lucy asked.

"Vasquez found a deleted file that showed Lillian couldn't stabilise the virus. But she figured out we would make a cure. So she came up with a way of using one of the enzymes manufactured in the cure to stabilise the virus."

"So she is using our solution to make the virus?" Lois asked.

"Yes." Alex confirmed.

"Does that make our cure useless?" Lucy asked.

"Yes." Alex stated grimly.

"That is proper evil genius." Winn commented turning round. "Um Alex."

"What?" She asked.

"Where's Kara?" He asked noticing her chair was empty.

"That idiot." Alex complained looking at the empty seat. "Where is she?"

"According to the radar heading to L-Corp." Winn said looking at some data on his screen.

"Radio J'onn and get him over there."

"What about Superman?" Winn asked.

"No. It's too dangerous, chances are Lillian has Kryptonite." Alex said. "Get him back here."

"Barnett is reporting they are under attack." Winn said. "Lena is deleting everything from the network, but they are keeping the cure in case this is a bluff."

"Where's the reinforcements?" Alex asked.

"The DEO team is four minutes out. J'onn is three minutes away and Kara is basically there."

-00-

As Supergirl flew into the lab Eliza asked.

"J'onn?"

"No. It's me." Kara said.

"What are you doing here?" Eliza asked dismayed.

"Cadmus is attacking." Kara said.

"Which is even more reason for you not to be here." Lena pointed out as she opened a cabinet.

"Is that a gun cabinet?" Kara asked.

"I don't think barbed insults are going to have much effect on my mother's goons." Lena pointed out as she offered Eliza a handgun.

"Kara you have to go." Eliza said. "It's not safe for you."

"I'm not leaving you." Kara argued.

"You really should have listened to your mother, well replacement mother." Lillian said walking into the lab. "Now your final act towards her won't be one of gratitude for all her sacrifices but defiance."

"Is it all adopted children you object to?" Lena asked.

"Just ingrates and aliens." Lillian said cooly as Kara stepped towards her. "I wouldn't do that if I were you." She said immediately causing Kara to pause. Lillian then pointed her finger over her shoulder. "Two of my well trained men have their weapons trained on those two." She said turning her hand and pointing towards Lena and Eliza. "One more step and they fire. And I doubt you are fast enough to stop bullets from both guns, especially in your weakened state. Unless you want to prove me wrong?"

When Kara took a step back Lillian smiled again and added. "You will make such an obedient pet. Unlike Lena." With that her expression turned cold and she looked at her daughter.

"Where is the cure?"

"We destroyed it." Lena said as Eliza backed away from the feuding Luthors.

"I could always tell when you were lying." Lillian said. "But even if I couldn't I raised you better than that. You don't know the information was real, it could have been a ploy to have you destroy the cure. You wouldn't take the risk. So where is it? Tell me and I'll let you choose who walks out of this room."

"What is it that makes you so insecure?" Eliza asked.

"I'm not insecure." Lillian said looking at Eliza. "What I do, I do because it is right." Lillian said as Lena used the distraction to take a few steps backwards.

"An argument plenty of genocidal dictators have used in the past." Eliza said.

"I don't have time to debate morals and ethics with a woman who destroyed her own daughter for the sake of an alien." Lillian said. "Now hand over the cure."

"Like Lena said we don't have it." Eliza said.

"If that is your final answer I will have to move to plan B." Lillian said. The statement causing the third armed guard she had with her to open a box. The action causing Kara to drop to her knees. "Assuming you did manage to remove the pellets I brought some more Kryptonite with me. Just normal green Kryptonite. Enough to weaken the alien into a mailable pet until I get her back to my lab." She said as the guard walked towards the fallen hero and placed a growing green collar round her neck.

"Leave her alone." Eliza demanded, although she did not step towards her daughter.

"Give me the cure." Lillian countered.

"We don't have it. It was never here." Lena said. "We were a decoy. The cure was made last night at the DEO."

"Lena? I really am disappointed in you. Giving in so easily, I expected more fight. You really must have seen the alien as your friend. So sad that she betrayed you. You really are destined to be alone." Lillian said before nodding at her guard who grabbed Kara's cape and dragged her from the room. She then looked at Eliza and said. "At least I know your brainwashed child will hand over the cure rather than watching the alien die." As she turned to leave an explosion rocked the lab.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	22. Chapter 22

**A/N:** Thanks for the comments.

 _Guest(1)_ \- I had forgotten that Andrew Kreisberg was fired this season - I can't believe that has all happened in the last year. That does explain some of the inconsistencies.

 _Guest(2)_ \- I am still hoping they don't Lena evil at all...or have a single episode where Winn and Lena are exposed to something that make them both evil, but only for the episode.

 _csiaddictfan87_ \- Thanks! I think that was the last cliffhanger.

* * *

Kara felt and heard the explosion but, even though she was released by her dazed captor, was too weak to do anything. Struggling to raise her arms she tried to pull off the collar but the Kryptonite got the better of her. Just as she was starting to loose consciousness she became aware of someone approaching. Forcing her neck up she saw Lillian stare down at her.

"This isn't over." Lillian said before walking off leaving Kara lying confused and alone on the floor.

Unable to keep her neck tilted anymore, Kara's head dropped back onto the cool surface and she shut her eyes as she drifted towards darkness. When she felt hands round her neck she tried to struggle, but could not muster enough strength and whoever was near her remained undeterred by her futile resistance.

Just as she was beginning to lose hope she felt the weight of the collar leave her moments before her strength started to return. Before she could figure out what was going on she was pulled into a familiar pair of arms. Still too drained to say anything she shut her eyes once more and drew comfort from the familiar voice near her head, although she couldn't focus enough to make out the words. Just as she was about to drift to sleep a sterner voice called her name, the tone causing her eyes to snap open.

"Come on Kara, you need to wake up." J'onn said, kneeling before her. "It isn't safe here and I can't carry all of you."

"All of us?" Kara asked confused as she tried to focus. Recalling the explosion she suddenly pulled out of the arms holding her and asked. "Eliza? Lena?"

"We're right here Sweetie." Eliza said pulling her back into her embrace.

"Lillian...she left." Kara said.

"We can worry about that later." J'onn said. "We need to move." He added before taking her hand and hauling her to her feet. As she unsteadily stood J'onn looked to Lena and said. "Lena, take the Kryptonite outside, we'll follow you."

Nodding, Lena grabbed the discarded Kryptonite collar and ran towards the outside world as J'onn and Eliza worked with Kara.

-00-

"What were you thinking?" Alex asked when she saw Kara, Lena, Eliza and J'onn enter the control room. "How could you be so stupid?"

"Pretty sure that is aimed at you." Lena prompted when Kara didn't immediately respond.

"It's not my fault they had Kryptonite." Kara protested.

"It's your fault for charing in there when you should be in the infirmary." Alex shot back at her.

"You would have been out there doing the same if you didn't have a huge hole in your side." Kara pointed out as she wavered unsteadily on her feet causing Eliza to take hold of Kara's arm.

"You are as bad as each other." Eliza commented her tone leaving no room for come back. "Come on, you need to go under the lamps and you are staying there all night. I don't care how uncomfortable the bed is." Eliza added sternly.

"Food would help me recover faster." Kara said optimistically as Eliza led her to the infirmary, followed by Alex.

"After what you did don't expect pizza or pie anytime soon." Eliza warned as they entered the lamp room where Hamilton was waiting.

"I need to check Kara is okay so why don't you all leave?" Hamilton suggested, immediately picking up on the anger radiating from Alex. "Unless you want to be a patient again." She said looking at Alex.

"We need to debrief anyway." J'onn said looking at Alex and Eliza.

"We'll be back soon." Eliza said as she hugged Kara. "Do not move from this room."

-00-

"What exactly happened?" Alex asked when they entered the briefing room, not even waiting for the others to greet Eliza

"Like you warned us, my mother attacked and tried to get the cure. But she failed." Lena said.

"Not without taking out the lab and nearly killing you all in the process." Alex pointed out.

"Technically she wasn't responsible for the explosion." Lena said.

"Then why it did it explode?" Alex asked.

"There was a failsafe installed."

"A failsafe?" Alex asked.

"The lab was rigged to blow when a switch was activated. The switch also threw up a forcefield round the central area which theoretically could withstand a large blast." Lena said. "We, your mother and I, were inside the forcefield when the explosion happened so were unscathed. My mother was unfortunately by the door when the explosion happened to apart from being knocked off her feet wasn't hurt."

"Where is she now?" Alex asked.

"Kara said she escaped." J'onn explained as Alex turned her attention back to Lena and asked, eyes wide.

"Wait. What do you mean the forcefield could theoretically withstand the blast? You didn't know?"

"No. I don't actually go round destroying my facilities." Lena said. "Then again apparently I don't need to, the DEO does it for me."

"Apart from today when you did it with my family there." Alex said glaring at Lena.

"Oh, no. That wasn't me. That was your mother."

"You blew the lab?" J'onn asked Eliza, beating Alex to the question.

"It seemed like the quickest way to get to Kara." Eliza said.

"I'm starting to wonder if there is something in the water in Midvale." Lucy said.

"What if the forcefield hadn't worked?" Alex asked, finding her voice again.

"I had no reason to believe it wouldn't." Eliza said. "Lena is more than competent. Now if you don't mind I need to talk to your sister about her poor decisions." She added walking off.

"Her poor decisions?" Alex asked in disbelief.

"I assume I can add the damage to the bill?" Lena asked as she too left.

-00-

"What were you thinking?" Eliza asked as she sat next to Kara.

"You were in danger I wanted to help."

"It wasn't safe." Eliza pointed out.

"Doesn't matter. You were in danger." Kara argued.

"You nearly died Kara." Eliza said, her voice wavering slightly. "You can't be so reckless. You have to think things through."

"I did. I couldn't let something happen to you." She said before looking away from Eliza and adding. "I have cost you and Alex so much already."

"Your actions nearly cost Alex her sister." Eliza snapped before calming herself and taking Kara's hand, adding. "You are my daughter and there are no debts in family. All we want is for you to be safe. I need you to promise me that you won't do anything like that again, because I can't lose you."

"I'm sorry for scaring you." Kara said squeezing Eliza's hand.

 **-TBC...**

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 **A/N:** Thanks for reading and reviewing.


	23. Chapter 23

**A/N:** Thanks for the comments.

 _csiaddictfan87_ : I have actually got a as yet unfinished and unpublished story where Lillian does get what's coming to her. But she'll get away with everything in this story.

 _Guest_ \- I meant more Winn and Lena would make a good, funny (if it was only for one episode) evil duo. I'm still rooting for Lena never turning bad though and breaking away from the cliches. Shooting starts soon so I guess it is not too long before rumours of the S4 big bad come out.

* * *

"So you and Superman seemed to be giving it your all in that fight." Alex commented as she joined J'onn in the briefing room the next day.

"We needed it to look realistic. If Lillian doubted it she may have accelerated her plans to release the virus."

"True, but you were really slugging it out. I thought you had buried your differences?"

"We have. As I said, it was just an act."

"Do Clark's ribs agree with you?" Alex asked.

"You'd have to ask his ribs." J'onn replied.

"I would if he was still here. But he left pretty quickly last night."

"He has responsibilities in Metropolis." J'onn reminded her before saying. "Assuming you have been working and not resting like I told you to, how sure are you that Lillian can't make the virus?"

"Without the enzyme in the cure we made, the virus degrades too quickly to be a threat. However, she seems to have eyes everywhere so it is probably only a matter of time before she can make her own version. What works in our favour is the fact she needs a very rare mineral to make it. A mineral that is only found in two mines in the world and we can track every shipment. The other good news is Winn thinks he can detect the spectral fingerprint of the virus, so if it is released we'll know quickly."

"We need to be careful not to get too focused on the virus. Knowing Lillian Luthor she'll use the threat of a virus as a distraction and blindside us with a new plan." J'onn commented before asking. "How are you doing?"

"Angry that Lillian got away, again. But I know dad is okay and free from her so there is a silver lining." Alex said.

"We've finished going through the database Vasquez downloaded." Winn said entering the room. "Sorry, am I interrupting?"

"No." Alex said. "What do you have?"

"There is no evidence to suggest she was involved in the attack on you." He started, looking at J'onn. "Which could be because she covered her tracks or because she really wasn't involved."

"So we still know nothing?" Alex said frustrated.

"I'm afraid so, but I will keep working on it. I have made some progress though." Winn said.

"What's that?"

"I have set up a monitor of the frequencies Lillian uses to talk to Kara. If she tries it again we'll know."

"Good." Alex said.

"What about the surveillance of Lena?" J'onn asked.

"Set up, and like you told me to I told her. She wasn't happy but realised she didn't have a choice."

"Hopefully it won't be needed." J'onn said before asking Alex. "Where's your sister?"

"Mom took her back to her apartment."

"You should go too. Take the next few days off."

-00-

"Kara? I wasn't expecting you. I'm surprised Alex let you out. Does she know you are out?" Lena greeted when Kara entered her office.

"She does." Kara said.

"How are you feeling?"

"Like I need to detox." Kara complained.

"By which I assume you mean pizza and sticky buns rather than spinach and nettle juice." Lena guessed.

"I've had way too much green stuff recently." Kara said. When Lena smiled but didn't speak Kara went on. "You're probably wondering why I'm here."

"Well I'm guessing it's not for my salad." Lena said looking at the unfinished plate on her desk.

"I wanted to say thank you."

"For what? It was you who saved me."

"Only after you saved me. You saved all the aliens on the planet and turned on your mother. And now you are in danger for helping me."

"I can recommend a therapist who helps with an oversized guilt complex." Lena said.

"This is serious." Kara said. "You are in danger. You need protection."

"Which the DEO is providing against my wishes."

"That may not be enough. It's not safe here." Kara argued.

"I am not going into hiding. If my mother wants to come after me, let her. It is better to have her out in the open rather than lingering in the shadows."

"Not if you get hurt or worse." Kara argued.

"Are you and Alex going into hiding?" Lena asked.

"No."

"Well then." Lena said. "I have been taking care of myself for a long time and I will continue to do so."

"I know. I just don't want you to get hurt any more than you already have." Kara said.

"I appreciate the concern, but I'll be okay." Lena replied before changing topics and asking. "Any news on your foster father?"

"No. Nothing." Kara replied. "But Alex won't stop searching for him. Can I ask you something?"

"Sure."

"Do you think Jeremiah was really on our side?"

"Why are you asking me?" Lena asked.

"You spent time with him and you have no preconceptions."

"I wouldn't go that far, my family has a lot of baggage which will shape my opinions."

"I'd still like to know what you think." Kara said. "I have always valued your opinions."

"He was helping you." Lena said.

"But?"

"But too much of his story didn't make sense. Even if you did come up with an explanation for every inconsistency in his story, he worked with my mother for years. No one comes away from that unscathed. I'm sorry."

"I asked." Kara said before standing. "I guess this is goodbye."

"Goodbye?" Lena asked.

"You said you could never be friends with someone who betrayed you."

"I did." Lena agreed. "But it was Supergirl who betrayed me. Not Kara Danvers."

"We're the same." Kara said.

"If that were true you wouldn't have two identities." Lena pointed out. "No matter what you say Kara Danvers and Supergirl are very different."

"I guess. I mean as Supergirl I can reach people, I can help people."

"Kara Danvers reaches thousands of people through her insightful yet optimistic articles. Don't get me wrong, I am very grateful to Supergirl, she has saved my life countless times. The World needs Supergirl." Lena said. "But it was always Kara Danvers that was my friend and my hero. She saved me in ways Supergirl never could. She listened rather than preached. I still need Kara Danvers."

"Can you really separate me from me?"

"Honestly, I don't know. But I'll try if you will."

-00-

"Hey." Kara greeted as she entered Alex's apartment. "Where's Eliza?"

"She went out to buy dinner." Alex replied. "How was Lena?"

"Okay." Kara said as she sat down next to her sister.

"Meaning?"

"She doesn't like Supergirl, but wants to be friends with Kara."

"Isn't that good?" Alex asked.

"What happens the next time Supergirl and Lena have to work together? Why does everything have to be so complicated?"

"You're an alien living on Earth, what do you expect?" Alex asked. "But you'll get your friendship back." She added before hugging her sister.

"I hope so." Kara said before pulling away and asking. "Can I get you anything?"

"A drink?"

"Water?"

"Not what I was thinking." Alex said.

"It's all I'm offering." Kara countered.

"In that case, I'm fine. Well bored." Alex said.

"So what have you done today?"

"Try to come up with as many errands as possible for mom so I got some peace."

"That's mean." Kara pointed out.

"It was the best option for both of us." Alex said. "And once she had gone I had plenty of time to think."

"About what?" Kara asked.

"Like, next time you decide you need time away, you do realise I'm not letting you go alone?"

"Trust me I don't want anytime alone." Kara said before asking "Can I stay here tonight?"

"Of course you can." Alex said ignoring the pain in her side and hugging her again. "But the next time a crazy person sends you a message telling you to fly straight into a trap, don't. And no more going off on missions without me."

"You know that I am going to be going on plenty of missions while you recover?" Kara asked.

"Not without J'onn you're not." Alex said as the two fell into a comfortable silence only to be broken by Kara.

"I'm sorry that you lost your dad again."

"Our dad." Alex corrected. "At least we know he is free from Cadmus."

"Yeah." Kara said non-committally.

"I can't even start to imagine what you went through, but you will get through this." Alex said misunderstanding Kara's lack of enthusiasm.

"Why didn't you call me when J'onn got hurt?" Kara asked.

"You needed time. I thought we could handle it."

"Do you know who was behind it yet?"

"No. There's no evidence to suggest it was Cadmus. But they are our only lead."

"Should J'onn be alone?" Kara asked.

"He's not. He has a team watching him."

"Does he know?" Kara asked.

"He's a physic so it was kinda hard to hide."

"And he's okay with it?"

"No. But he knows the only way I'll take time off is if he agrees." Alex said.

"And when you return to work?"

"Then Guardian is going to keep an eye on him. Hopefully that way J'onn can keep James out of trouble too." Alex explained as the door opened and Eliza walked in carrying bags of food.

"How are my favourite girls?" She asked as she put the bags down.

"Favourite? Does that mean we're forgiven?" Kara asked optimistically as she moved over and hugged Eliza.

"Like you are ever in trouble for long." Alex muttered.

"Right now you are both still in trouble." Eliza warned.

"You do remember it was you who blew up a room when you were still inside?" Alex asked.

"You two need to take better care of yourselves." Eliza said ignoring her eldest.

"We will." Kara promised her as she started to unpack the bags. As she did so her eyes lit up. "Chocolate, pecans, flour, does this mean you are making chocolate pecan pie?"

"Seriously?" Alex asked. "Kara's in trouble and still gets her favourite pie?"

Smiling Eliza picked up a small bag and went towards the couch. Kissing Alex on the top of her head she said.

"I have something for you too."

"You do?" Alex asked surprised.

"I know you can probably get it on Netflix, but a real copy seemed better." Eliza said giving Alex the bag.

"I love this film." Alex said pulling 'The Shining' from the bag. "We are so watching this tonight."

"I hate that film." Kara said. "Wait is this my punishment? You are going to make me watch it."

"Don't be such a baby." Alex said throwing a cushion at Kara before adding. "I'll look after you."

 **-The End**

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 **A/N:** Thanks for reading and reviewing. I hope you enjoyed it.


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